├── .gitattributes ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── deploy_anaconda.sh ├── docs ├── CGI_Finder │ ├── API_usage.ipynb │ ├── CLI_usage.ipynb │ └── usage.md ├── Comp_Report │ ├── API_usage.ipynb │ ├── CLI_usage.ipynb │ ├── human_html │ │ ├── interval_reports │ │ │ ├── interval_0001_chr19-1465074-1471294.html │ │ │ ├── interval_0002_chr5-171313349-171317243.html │ │ │ ├── interval_0003_chr16-54936192-54939415.html │ │ │ ├── interval_0004_chr5-141430472-141433184.html │ │ │ ├── interval_0005_chr1-145167533-145169830.html │ │ │ ├── interval_0006_chr14-69571220-69573973.html │ │ │ ├── interval_0007_chr7-149764357-149766480.html │ │ │ ├── interval_0008_chr4-1001583-1003754.html │ │ │ ├── interval_0009_chr17-61403712-61405954.html │ │ │ ├── interval_0010_chr8-140097670-140099673.html │ │ │ ├── interval_0011_chr17-72116370-72118672.html │ │ │ ├── interval_0012_chr12-57737069-57739227.html │ │ │ ├── interval_0013_chr19-13097401-13099852.html │ │ │ ├── interval_0014_chr17-83133989-83135844.html │ │ │ ├── interval_0015_chr20-20363429-20365644.html │ │ │ ├── interval_0016_chr16-693807-696068.html │ │ │ ├── interval_0017_chr5-2748080-2750204.html │ │ │ ├── interval_0018_chr2-66445077-66447024.html │ │ │ ├── interval_0019_chr6-108174295-108176232.html │ │ │ ├── interval_0020_chr19-44756986-44758607.html │ │ │ ├── interval_0021_chr1-180234214-180236317.html │ │ │ ├── interval_0022_chr7-155453612-155455178.html │ │ │ ├── interval_0023_chr19-46493059-46495487.html │ │ │ ├── interval_0024_chr4-80201275-80203807.html │ │ │ ├── interval_0025_chr18-57439921-57441962.html │ │ │ ├── interval_0026_chr17-64780064-64781774.html │ │ │ ├── interval_0027_chr19-40612973-40614827.html │ │ │ ├── interval_0028_chr6-137487832-137489432.html │ │ │ ├── interval_0029_chrX-21655641-21659118.html │ │ │ ├── interval_0030_chr11-65646176-65647982.html │ │ │ ├── interval_0031_chr4-8856713-8858934.html │ │ │ ├── interval_0032_chr5-141491307-141492957.html │ │ │ ├── interval_0033_chr15-52794405-52796114.html │ │ │ ├── interval_0034_chr6-1392675-1394273.html │ │ │ ├── interval_0035_chr9-127754034-127755653.html │ │ │ ├── interval_0036_chr22-27796653-27799585.html │ │ │ ├── interval_0037_chr5-93571867-93573562.html │ │ │ ├── interval_0038_chr22-19765660-19767542.html │ │ │ ├── interval_0039_chr20-46057007-46058998.html │ │ │ ├── interval_0040_chr22-19722855-19724692.html │ │ │ ├── interval_0041_chr17-79814738-79816386.html │ │ │ ├── interval_0042_chr7-989495-990877.html │ │ │ ├── interval_0043_chr2-130692515-130693970.html │ │ │ ├── interval_0044_chr17-81527850-81529362.html │ │ │ ├── interval_0045_chrX-1465367-1466722.html │ │ │ ├── interval_0046_chr12-57726081-57727919.html │ │ │ ├── interval_0047_chr5-177984160-177986165.html │ │ │ ├── interval_0048_chr19-3648956-3650054.html │ │ │ ├── interval_0049_chr8-143278147-143279510.html │ │ │ ├── interval_0050_chrX-48826215-48827761.html │ │ │ ├── interval_0051_chr10-99521271-99522611.html │ │ │ ├── interval_0052_chr1-976586-978571.html │ │ │ ├── interval_0053_chr9-124014988-124016512.html │ │ │ ├── interval_0054_chr5-6773361-6774577.html │ │ │ ├── interval_0055_chr19-15457038-15458549.html │ │ │ ├── interval_0056_chr9-137450268-137452038.html │ │ │ ├── interval_0057_chr2-154698540-154699822.html │ │ │ ├── interval_0058_chr19-17328027-17329755.html │ │ │ ├── interval_0059_chr4-8866964-8868473.html │ │ │ ├── interval_0060_chr15-89408959-89410257.html │ │ │ ├── interval_0061_chr7-767536-768780.html │ │ │ ├── interval_0062_chr22-23838197-23839612.html │ │ │ ├── interval_0063_chr16-49277180-49278574.html │ │ │ ├── interval_0064_chr17-28384274-28385453.html │ │ │ ├── interval_0065_chr7-27141823-27143630.html │ │ │ ├── interval_0066_chr5-3601878-3603265.html │ │ │ ├── interval_0067_chr17-48550301-48551868.html │ │ │ ├── interval_0068_chr15-65395552-65397126.html │ │ │ ├── interval_0069_chr2-176066755-176068252.html │ │ │ ├── interval_0070_chr1-3062986-3064284.html │ │ │ ├── interval_0071_chr3-194396715-194398455.html │ │ │ ├── interval_0072_chr16-54288263-54289879.html │ │ │ ├── interval_0073_chr5-3599098-3600332.html │ │ │ ├── interval_0074_chr19-58355910-58357548.html │ │ │ ├── interval_0075_chr10-93059948-93061756.html │ │ │ ├── interval_0076_chr15-89378319-89379811.html │ │ │ ├── interval_0077_chr18-5890207-5891836.html │ │ │ ├── interval_0078_chr21-46160485-46162232.html │ │ │ ├── interval_0079_chr16-2236530-2238140.html │ │ │ ├── interval_0080_chr10-86363012-86364273.html │ │ │ ├── interval_0081_chr10-133166368-133167794.html │ │ │ ├── interval_0082_chr5-177366903-177367884.html │ │ │ ├── interval_0083_chr16-88634016-88635175.html │ │ │ ├── interval_0084_chr16-67652623-67654020.html │ │ │ ├── interval_0085_chr15-82679964-82681226.html │ │ │ ├── interval_0086_chr16-912164-913539.html │ │ │ ├── interval_0087_chr19-1070971-1072321.html │ │ │ ├── interval_0088_chr15-89406944-89408372.html │ │ │ ├── interval_0089_chr16-54281497-54282666.html │ │ │ ├── interval_0090_chr8-140099765-140101001.html │ │ │ ├── interval_0091_chr17-45428957-45431152.html │ │ │ ├── interval_0092_chr19-47446997-47448525.html │ │ │ ├── interval_0093_chr1-203075448-203076659.html │ │ │ ├── interval_0094_chr17-45240959-45242226.html │ │ │ ├── interval_0095_chr2-172080093-172081574.html │ │ │ ├── interval_0096_chr1-1332513-1333703.html │ │ │ ├── interval_0097_chr19-17841311-17842723.html │ │ │ ├── interval_0098_chr19-5058595-5059854.html │ │ │ ├── interval_0099_chr8-9898069-9899160.html │ │ │ ├── interval_0100_chr10-48450148-48451244.html │ │ │ ├── interval_0101_chr1-43348388-43349760.html │ │ │ ├── interval_0102_chr17-61456303-61457574.html │ │ │ ├── interval_0103_chr1-90835271-90836499.html │ │ │ ├── interval_0104_chr2-156319615-156320997.html │ │ │ ├── interval_0105_chr12-80707849-80709118.html │ │ │ ├── interval_0106_chr19-46648377-46650496.html │ │ │ ├── interval_0107_chr19-18777071-18778254.html │ │ │ ├── interval_0108_chrX-3346387-3347488.html │ │ │ ├── interval_0109_chr3-50275125-50277017.html │ │ │ ├── interval_0110_chr10-75395143-75397856.html │ │ │ ├── interval_0111_chr12-132270984-132272270.html │ │ │ ├── interval_0112_chr10-92690986-92692269.html │ │ │ ├── interval_0113_chr1-18482252-18483305.html │ │ │ ├── interval_0114_chr6-3224545-3225483.html │ │ │ ├── interval_0115_chr22-50719863-50721434.html │ │ │ ├── interval_0116_chr7-27251341-27252745.html │ │ │ ├── interval_0117_chr1-217137129-217138574.html │ │ │ ├── interval_0118_chr19-13962302-13964169.html │ │ │ ├── interval_0119_chr5-73230217-73231331.html │ │ │ ├── interval_0120_chr19-8525815-8527115.html │ │ │ ├── interval_0121_chr7-102494140-102495276.html │ │ │ ├── interval_0122_chr12-132835523-132836850.html │ │ │ ├── interval_0123_chr13-50132274-50133978.html │ │ │ ├── interval_0124_chr16-1019132-1020232.html │ │ │ ├── interval_0125_chr16-55330647-55332251.html │ │ │ ├── interval_0126_chr13-114043702-114044738.html │ │ │ ├── interval_0127_chr5-93570321-93571592.html │ │ │ ├── interval_0128_chr5-11384413-11385577.html │ │ │ ├── interval_0129_chr13-113729703-113730407.html │ │ │ ├── interval_0130_chr17-74356576-74357824.html │ │ │ ├── interval_0131_chr19-48442368-48444808.html │ │ │ ├── interval_0132_chr12-54018428-54019691.html │ │ │ ├── interval_0133_chr11-118609436-118611360.html │ │ │ ├── interval_0134_chr11-979911-980652.html │ │ │ ├── interval_0135_chr20-40682660-40683906.html │ │ │ ├── interval_0136_chr8-902134-903249.html │ │ │ ├── interval_0137_chr1-16646922-16648717.html │ │ │ ├── interval_0138_chr2-70888459-70889814.html │ │ │ ├── interval_0139_chr3-9945833-9948110.html │ │ │ ├── interval_0140_chr19-49337904-49339149.html │ │ │ ├── interval_0141_chr19-7868132-7870134.html │ │ │ ├── interval_0142_chr8-41566734-41567976.html │ │ │ ├── interval_0143_chr7-102593401-102594445.html │ │ │ ├── interval_0144_chr21-39385121-39386159.html │ │ │ ├── interval_0145_chr13-99996875-99998262.html │ │ │ ├── interval_0146_chr13-113820374-113821613.html │ │ │ ├── interval_0147_chr2-44944047-44945194.html │ │ │ ├── interval_0148_chr5-179974119-179975388.html │ │ │ ├── interval_0149_chr6-10417025-10418033.html │ │ │ ├── interval_0150_chr17-61454234-61455475.html │ │ │ ├── interval_0151_chr2-219447906-219449258.html │ │ │ ├── interval_0152_chr14-56797809-56798963.html │ │ │ ├── interval_0153_chr19-18869785-18870857.html │ │ │ ├── interval_0154_chr7-128915264-128916729.html │ │ │ ├── interval_0155_chr17-44314868-44316217.html │ │ │ ├── interval_0156_chr16-4380941-4382016.html │ │ │ ├── interval_0157_chr19-6475043-6476116.html │ │ │ ├── interval_0158_chr2-104866992-104868029.html │ │ │ ├── interval_0159_chr10-43395730-43397662.html │ │ │ ├── interval_0160_chr11-113314191-113315414.html │ │ │ ├── interval_0161_chr8-144547649-144548633.html │ │ │ ├── interval_0162_chr2-236159308-236160358.html │ │ │ ├── interval_0163_chr5-159104866-159105808.html │ │ │ ├── interval_0164_chr13-99988942-99990064.html │ │ │ ├── interval_0165_chr6-35317842-35318953.html │ │ │ ├── interval_0166_chr11-128689675-128690759.html │ │ │ ├── interval_0167_chr10-101778627-101780425.html │ │ │ ├── interval_0168_chr11-60950585-60952014.html │ │ │ ├── interval_0169_chr6-27830671-27831771.html │ │ │ ├── interval_0170_chr17-31008224-31009540.html │ │ │ ├── interval_0171_chrX-40091300-40092577.html │ │ │ ├── interval_0172_chr15-93065800-93066857.html │ │ │ ├── interval_0173_chr12-49263835-49265711.html │ │ │ ├── interval_0174_chr14-73718430-73719600.html │ │ │ ├── interval_0175_chr1-229407010-229408217.html │ │ │ ├── interval_0176_chr19-53554050-53555123.html │ │ │ ├── interval_0177_chr7-157500761-157501976.html │ │ │ ├── interval_0178_chr10-2935661-2936694.html │ │ │ ├── interval_0179_chr2-104863596-104864466.html │ │ │ ├── interval_0180_chr6-26188238-26189254.html │ │ │ ├── interval_0181_chr5-3606229-3607148.html │ │ │ ├── interval_0182_chr17-45261651-45262576.html │ │ │ ├── interval_0183_chr2-63059286-63060202.html │ │ │ ├── interval_0184_chr15-28454584-28455597.html │ │ │ ├── interval_0185_chr5-141414667-141415625.html │ │ │ ├── interval_0186_chr7-150322740-150324008.html │ │ │ ├── interval_0187_chr5-173228696-173229703.html │ │ │ ├── interval_0188_chr12-57224680-57225762.html │ │ │ ├── interval_0189_chr17-79802607-79803543.html │ │ │ ├── interval_0190_chr16-31475670-31477781.html │ │ │ ├── interval_0191_chr7-27113387-27114325.html │ │ │ ├── interval_0192_chr3-50364514-50365648.html │ │ │ ├── interval_0193_chr7-5295984-5297370.html │ │ │ ├── interval_0194_chr6-137495170-137496226.html │ │ │ ├── interval_0195_chr4-576907-578189.html │ │ │ ├── interval_0196_chr1-90719323-90720202.html │ │ │ ├── interval_0197_chr7-44962443-44963350.html │ │ │ ├── interval_0198_chr16-67165262-67166195.html │ │ │ ├── interval_0199_chr11-22340923-22341888.html │ │ │ └── interval_0200_chr7-25852165-25853174.html │ │ ├── interval_tables │ │ │ ├── interval_0001_chr19-1465074-1471294.tsv │ │ │ ├── interval_0002_chr5-171313349-171317243.tsv │ │ │ ├── interval_0003_chr16-54936192-54939415.tsv │ │ │ ├── interval_0004_chr5-141430472-141433184.tsv │ │ │ ├── interval_0005_chr1-145167533-145169830.tsv │ │ │ ├── interval_0006_chr14-69571220-69573973.tsv │ │ │ ├── interval_0007_chr7-149764357-149766480.tsv │ │ │ ├── interval_0008_chr4-1001583-1003754.tsv │ │ │ ├── interval_0009_chr17-61403712-61405954.tsv │ │ │ ├── interval_0010_chr8-140097670-140099673.tsv │ │ │ ├── interval_0011_chr17-72116370-72118672.tsv │ │ │ ├── interval_0012_chr12-57737069-57739227.tsv │ │ │ ├── interval_0013_chr19-13097401-13099852.tsv │ │ │ ├── interval_0014_chr17-83133989-83135844.tsv │ │ │ ├── interval_0015_chr20-20363429-20365644.tsv │ │ │ ├── interval_0016_chr16-693807-696068.tsv │ │ │ ├── interval_0017_chr5-2748080-2750204.tsv │ │ │ ├── interval_0018_chr2-66445077-66447024.tsv │ │ │ ├── interval_0019_chr6-108174295-108176232.tsv │ │ │ ├── interval_0020_chr19-44756986-44758607.tsv │ │ │ ├── interval_0021_chr1-180234214-180236317.tsv │ │ │ ├── interval_0022_chr7-155453612-155455178.tsv │ │ │ ├── interval_0023_chr19-46493059-46495487.tsv │ │ │ ├── interval_0024_chr4-80201275-80203807.tsv │ │ │ ├── interval_0025_chr18-57439921-57441962.tsv │ │ │ ├── interval_0026_chr17-64780064-64781774.tsv │ │ │ ├── interval_0027_chr19-40612973-40614827.tsv │ │ │ ├── interval_0028_chr6-137487832-137489432.tsv │ │ │ ├── interval_0029_chrX-21655641-21659118.tsv │ │ │ ├── interval_0030_chr11-65646176-65647982.tsv │ │ │ ├── interval_0031_chr4-8856713-8858934.tsv │ │ │ ├── interval_0032_chr5-141491307-141492957.tsv │ │ │ ├── interval_0033_chr15-52794405-52796114.tsv │ │ │ ├── interval_0034_chr6-1392675-1394273.tsv │ │ │ ├── interval_0035_chr9-127754034-127755653.tsv │ │ │ ├── interval_0036_chr22-27796653-27799585.tsv │ │ │ ├── interval_0037_chr5-93571867-93573562.tsv │ │ │ ├── interval_0038_chr22-19765660-19767542.tsv │ │ │ ├── interval_0039_chr20-46057007-46058998.tsv │ │ │ ├── interval_0040_chr22-19722855-19724692.tsv │ │ │ ├── interval_0041_chr17-79814738-79816386.tsv │ │ │ ├── interval_0042_chr7-989495-990877.tsv │ │ │ ├── interval_0043_chr2-130692515-130693970.tsv │ │ │ ├── interval_0044_chr17-81527850-81529362.tsv │ │ │ ├── interval_0045_chrX-1465367-1466722.tsv │ │ │ ├── interval_0046_chr12-57726081-57727919.tsv │ │ │ ├── interval_0047_chr5-177984160-177986165.tsv │ │ │ ├── interval_0048_chr19-3648956-3650054.tsv │ │ │ ├── interval_0049_chr8-143278147-143279510.tsv │ │ │ ├── interval_0050_chrX-48826215-48827761.tsv │ │ │ ├── interval_0051_chr10-99521271-99522611.tsv │ │ │ ├── interval_0052_chr1-976586-978571.tsv │ │ │ ├── interval_0053_chr9-124014988-124016512.tsv │ │ │ ├── interval_0054_chr5-6773361-6774577.tsv │ │ │ ├── interval_0055_chr19-15457038-15458549.tsv │ │ │ ├── interval_0056_chr9-137450268-137452038.tsv │ │ │ ├── interval_0057_chr2-154698540-154699822.tsv │ │ │ ├── interval_0058_chr19-17328027-17329755.tsv │ │ │ ├── interval_0059_chr4-8866964-8868473.tsv │ │ │ ├── interval_0060_chr15-89408959-89410257.tsv │ │ │ ├── interval_0061_chr7-767536-768780.tsv │ │ │ ├── interval_0062_chr22-23838197-23839612.tsv │ │ │ ├── interval_0063_chr16-49277180-49278574.tsv │ │ │ ├── interval_0064_chr17-28384274-28385453.tsv │ │ │ ├── interval_0065_chr7-27141823-27143630.tsv │ │ │ ├── interval_0066_chr5-3601878-3603265.tsv │ │ │ ├── interval_0067_chr17-48550301-48551868.tsv │ │ │ ├── interval_0068_chr15-65395552-65397126.tsv │ │ │ ├── interval_0069_chr2-176066755-176068252.tsv │ │ │ ├── interval_0070_chr1-3062986-3064284.tsv │ │ │ ├── interval_0071_chr3-194396715-194398455.tsv │ │ │ ├── interval_0072_chr16-54288263-54289879.tsv │ │ │ ├── interval_0073_chr5-3599098-3600332.tsv │ │ │ ├── interval_0074_chr19-58355910-58357548.tsv │ │ │ ├── interval_0075_chr10-93059948-93061756.tsv │ │ │ ├── interval_0076_chr15-89378319-89379811.tsv │ │ │ ├── interval_0077_chr18-5890207-5891836.tsv │ │ │ ├── interval_0078_chr21-46160485-46162232.tsv │ │ │ ├── interval_0079_chr16-2236530-2238140.tsv │ │ │ ├── interval_0080_chr10-86363012-86364273.tsv │ │ │ ├── interval_0081_chr10-133166368-133167794.tsv │ │ │ ├── interval_0082_chr5-177366903-177367884.tsv │ │ │ ├── interval_0083_chr16-88634016-88635175.tsv │ │ │ ├── interval_0084_chr16-67652623-67654020.tsv │ │ │ ├── interval_0085_chr15-82679964-82681226.tsv │ │ │ ├── interval_0086_chr16-912164-913539.tsv │ │ │ ├── interval_0087_chr19-1070971-1072321.tsv │ │ │ ├── interval_0088_chr15-89406944-89408372.tsv │ │ │ ├── interval_0089_chr16-54281497-54282666.tsv │ │ │ ├── interval_0090_chr8-140099765-140101001.tsv │ │ │ ├── interval_0091_chr17-45428957-45431152.tsv │ │ │ ├── interval_0092_chr19-47446997-47448525.tsv │ │ │ ├── interval_0093_chr1-203075448-203076659.tsv │ │ │ ├── interval_0094_chr17-45240959-45242226.tsv │ │ │ ├── interval_0095_chr2-172080093-172081574.tsv │ │ │ ├── interval_0096_chr1-1332513-1333703.tsv │ │ │ ├── interval_0097_chr19-17841311-17842723.tsv │ │ │ ├── interval_0098_chr19-5058595-5059854.tsv │ │ │ ├── interval_0099_chr8-9898069-9899160.tsv │ │ │ ├── interval_0100_chr10-48450148-48451244.tsv │ │ │ ├── interval_0101_chr1-43348388-43349760.tsv │ │ │ ├── interval_0102_chr17-61456303-61457574.tsv │ │ │ ├── interval_0103_chr1-90835271-90836499.tsv │ │ │ ├── interval_0104_chr2-156319615-156320997.tsv │ │ │ ├── interval_0105_chr12-80707849-80709118.tsv │ │ │ ├── interval_0106_chr19-46648377-46650496.tsv │ │ │ ├── interval_0107_chr19-18777071-18778254.tsv │ │ │ ├── interval_0108_chrX-3346387-3347488.tsv │ │ │ ├── interval_0109_chr3-50275125-50277017.tsv │ │ │ ├── interval_0110_chr10-75395143-75397856.tsv │ │ │ ├── interval_0111_chr12-132270984-132272270.tsv │ │ │ ├── interval_0112_chr10-92690986-92692269.tsv │ │ │ ├── interval_0113_chr1-18482252-18483305.tsv │ │ │ ├── interval_0114_chr6-3224545-3225483.tsv │ │ │ ├── interval_0115_chr22-50719863-50721434.tsv │ │ │ ├── interval_0116_chr7-27251341-27252745.tsv │ │ │ ├── interval_0117_chr1-217137129-217138574.tsv │ │ │ ├── interval_0118_chr19-13962302-13964169.tsv │ │ │ ├── interval_0119_chr5-73230217-73231331.tsv │ │ │ ├── interval_0120_chr19-8525815-8527115.tsv │ │ │ ├── interval_0121_chr7-102494140-102495276.tsv │ │ │ ├── interval_0122_chr12-132835523-132836850.tsv │ │ │ ├── interval_0123_chr13-50132274-50133978.tsv │ │ │ ├── interval_0124_chr16-1019132-1020232.tsv │ │ │ ├── interval_0125_chr16-55330647-55332251.tsv │ │ │ ├── interval_0126_chr13-114043702-114044738.tsv │ │ │ ├── interval_0127_chr5-93570321-93571592.tsv │ │ │ ├── interval_0128_chr5-11384413-11385577.tsv │ │ │ ├── interval_0129_chr13-113729703-113730407.tsv │ │ │ ├── interval_0130_chr17-74356576-74357824.tsv │ │ │ ├── interval_0131_chr19-48442368-48444808.tsv │ │ │ ├── interval_0132_chr12-54018428-54019691.tsv │ │ │ ├── interval_0133_chr11-118609436-118611360.tsv │ │ │ ├── interval_0134_chr11-979911-980652.tsv │ │ │ ├── interval_0135_chr20-40682660-40683906.tsv │ │ │ ├── interval_0136_chr8-902134-903249.tsv │ │ │ ├── interval_0137_chr1-16646922-16648717.tsv │ │ │ ├── interval_0138_chr2-70888459-70889814.tsv │ │ │ ├── interval_0139_chr3-9945833-9948110.tsv │ │ │ ├── interval_0140_chr19-49337904-49339149.tsv │ │ │ ├── interval_0141_chr19-7868132-7870134.tsv │ │ │ ├── interval_0142_chr8-41566734-41567976.tsv │ │ │ ├── interval_0143_chr7-102593401-102594445.tsv │ │ │ ├── interval_0144_chr21-39385121-39386159.tsv │ │ │ ├── interval_0145_chr13-99996875-99998262.tsv │ │ │ ├── interval_0146_chr13-113820374-113821613.tsv │ │ │ ├── interval_0147_chr2-44944047-44945194.tsv │ │ │ ├── interval_0148_chr5-179974119-179975388.tsv │ │ │ ├── interval_0149_chr6-10417025-10418033.tsv │ │ │ ├── interval_0150_chr17-61454234-61455475.tsv │ │ │ ├── interval_0151_chr2-219447906-219449258.tsv │ │ │ ├── interval_0152_chr14-56797809-56798963.tsv │ │ │ ├── interval_0153_chr19-18869785-18870857.tsv │ │ │ ├── interval_0154_chr7-128915264-128916729.tsv │ │ │ ├── interval_0155_chr17-44314868-44316217.tsv │ │ │ ├── interval_0156_chr16-4380941-4382016.tsv │ │ │ ├── interval_0157_chr19-6475043-6476116.tsv │ │ │ ├── interval_0158_chr2-104866992-104868029.tsv │ │ │ ├── interval_0159_chr10-43395730-43397662.tsv │ │ │ ├── interval_0160_chr11-113314191-113315414.tsv │ │ │ ├── interval_0161_chr8-144547649-144548633.tsv │ │ │ ├── interval_0162_chr2-236159308-236160358.tsv │ │ │ ├── interval_0163_chr5-159104866-159105808.tsv │ │ │ ├── interval_0164_chr13-99988942-99990064.tsv │ │ │ ├── interval_0165_chr6-35317842-35318953.tsv │ │ │ ├── interval_0166_chr11-128689675-128690759.tsv │ │ │ ├── interval_0167_chr10-101778627-101780425.tsv │ │ │ ├── interval_0168_chr11-60950585-60952014.tsv │ │ │ ├── interval_0169_chr6-27830671-27831771.tsv │ │ │ ├── interval_0170_chr17-31008224-31009540.tsv │ │ │ ├── interval_0171_chrX-40091300-40092577.tsv │ │ │ ├── interval_0172_chr15-93065800-93066857.tsv │ │ │ ├── interval_0173_chr12-49263835-49265711.tsv │ │ │ ├── interval_0174_chr14-73718430-73719600.tsv │ │ │ ├── interval_0175_chr1-229407010-229408217.tsv │ │ │ ├── interval_0176_chr19-53554050-53555123.tsv │ │ │ ├── interval_0177_chr7-157500761-157501976.tsv │ │ │ ├── interval_0178_chr10-2935661-2936694.tsv │ │ │ ├── interval_0179_chr2-104863596-104864466.tsv │ │ │ ├── interval_0180_chr6-26188238-26189254.tsv │ │ │ ├── interval_0181_chr5-3606229-3607148.tsv │ │ │ ├── interval_0182_chr17-45261651-45262576.tsv │ │ │ ├── interval_0183_chr2-63059286-63060202.tsv │ │ │ ├── interval_0184_chr15-28454584-28455597.tsv │ │ │ ├── interval_0185_chr5-141414667-141415625.tsv │ │ │ ├── interval_0186_chr7-150322740-150324008.tsv │ │ │ ├── interval_0187_chr5-173228696-173229703.tsv │ │ │ ├── interval_0188_chr12-57224680-57225762.tsv │ │ │ ├── interval_0189_chr17-79802607-79803543.tsv │ │ │ ├── interval_0190_chr16-31475670-31477781.tsv │ │ │ ├── interval_0191_chr7-27113387-27114325.tsv │ │ │ ├── interval_0192_chr3-50364514-50365648.tsv │ │ │ ├── interval_0193_chr7-5295984-5297370.tsv │ │ │ ├── interval_0194_chr6-137495170-137496226.tsv │ │ │ ├── interval_0195_chr4-576907-578189.tsv │ │ │ ├── interval_0196_chr1-90719323-90720202.tsv │ │ │ ├── interval_0197_chr7-44962443-44963350.tsv │ │ │ ├── interval_0198_chr16-67165262-67166195.tsv │ │ │ ├── interval_0199_chr11-22340923-22341888.tsv │ │ │ └── interval_0200_chr7-25852165-25853174.tsv │ │ ├── out_stderr.txt │ │ ├── out_stdout.txt │ │ ├── pycoMeth_summary_report.html │ │ └── pycoMeth_top_intervals.tsv │ ├── medaka_html │ │ ├── interval_reports │ │ │ ├── interval_0001_chr15-13014693-13015794.html │ │ │ ├── interval_0002_chr16-26220047-26221325.html │ │ │ ├── interval_0003_chr17-316390-318610.html │ │ │ ├── interval_0004_chr11-27686928-27688355.html │ │ │ ├── interval_0005_chr4-7874048-7875618.html │ │ │ ├── interval_0006_chr15-1565040-1565987.html │ │ │ ├── interval_0007_chr2-23361417-23362425.html │ │ │ ├── interval_0008_chr2-12169442-12171060.html │ │ │ ├── interval_0009_chr8-450569-451548.html │ │ │ ├── interval_0010_chr8-23224550-23225428.html │ │ │ ├── interval_0011_chr2-3660038-3660922.html │ │ │ ├── interval_0012_chr22-1816785-1817685.html │ │ │ ├── interval_0013_chr16-7720134-7721846.html │ │ │ ├── interval_0014_chr5-19638728-19639909.html │ │ │ ├── interval_0015_chr14-24222331-24223586.html │ │ │ ├── interval_0016_chr20-15042642-15043458.html │ │ │ ├── interval_0017_chr3-309650-310584.html │ │ │ ├── interval_0018_chr19-1948176-1949405.html │ │ │ ├── interval_0019_chr14-29614617-29615705.html │ │ │ ├── interval_0020_chr22-2405753-2407192.html │ │ │ ├── interval_0021_chr16-7663486-7664331.html │ │ │ ├── interval_0022_chr9-1939074-1940052.html │ │ │ ├── interval_0023_chr17-48535-49910.html │ │ │ ├── interval_0024_chr2-22706556-22707650.html │ │ │ ├── interval_0025_chr2-23324373-23325538.html │ │ │ ├── interval_0026_chr12-2187537-2190115.html │ │ │ ├── interval_0027_chr5-30060867-30062266.html │ │ │ ├── interval_0028_chr6-1003683-1004493.html │ │ │ ├── interval_0029_chr3-7956996-7957867.html │ │ │ ├── interval_0030_chr14-29286331-29287419.html │ │ │ ├── interval_0031_chr7-26640756-26641574.html │ │ │ ├── interval_0032_chr6-4948049-4949056.html │ │ │ ├── interval_0033_chr9-1940281-1941248.html │ │ │ ├── interval_0034_chr14-19955750-19956691.html │ │ │ ├── interval_0035_chr6-2209392-2211073.html │ │ │ ├── interval_0036_chr1-1608911-1609767.html │ │ │ ├── interval_0037_chr11-14611139-14611909.html │ │ │ ├── interval_0038_chr18-19963184-19964018.html │ │ │ ├── interval_0039_chr24-10286328-10287069.html │ │ │ ├── interval_0040_chr1-28861433-28862812.html │ │ │ ├── interval_0041_chr1-28858118-28859215.html │ │ │ ├── interval_0042_chr3-16474087-16474976.html │ │ │ ├── interval_0043_chr23-3850204-3850968.html │ │ │ ├── interval_0044_chr15-29821056-29822141.html │ │ │ ├── interval_0045_chr13-383208-383975.html │ │ │ ├── interval_0046_chr8-21261846-21262796.html │ │ │ ├── interval_0047_chr10-1395471-1396245.html │ │ │ ├── interval_0048_chr23-22979232-22979976.html │ │ │ ├── interval_0049_chr16-27924435-27925464.html │ │ │ └── interval_0050_chr21-28550521-28551558.html │ │ ├── interval_tables │ │ │ ├── interval_0001_chr15-13014693-13015794.tsv │ │ │ ├── interval_0002_chr16-26220047-26221325.tsv │ │ │ ├── interval_0003_chr17-316390-318610.tsv │ │ │ ├── interval_0004_chr11-27686928-27688355.tsv │ │ │ ├── interval_0005_chr4-7874048-7875618.tsv │ │ │ ├── interval_0006_chr15-1565040-1565987.tsv │ │ │ ├── interval_0007_chr2-23361417-23362425.tsv │ │ │ ├── interval_0008_chr2-12169442-12171060.tsv │ │ │ ├── interval_0009_chr8-450569-451548.tsv │ │ │ ├── interval_0010_chr8-23224550-23225428.tsv │ │ │ ├── interval_0011_chr2-3660038-3660922.tsv │ │ │ ├── interval_0012_chr22-1816785-1817685.tsv │ │ │ ├── interval_0013_chr16-7720134-7721846.tsv │ │ │ ├── interval_0014_chr5-19638728-19639909.tsv │ │ │ ├── interval_0015_chr14-24222331-24223586.tsv │ │ │ ├── interval_0016_chr20-15042642-15043458.tsv │ │ │ ├── interval_0017_chr3-309650-310584.tsv │ │ │ ├── interval_0018_chr19-1948176-1949405.tsv │ │ │ ├── interval_0019_chr14-29614617-29615705.tsv │ │ │ ├── interval_0020_chr22-2405753-2407192.tsv │ │ │ ├── interval_0021_chr16-7663486-7664331.tsv │ │ │ ├── interval_0022_chr9-1939074-1940052.tsv │ │ │ ├── interval_0024_chr2-22706556-22707650.tsv │ │ │ ├── interval_0025_chr2-23324373-23325538.tsv │ │ │ ├── interval_0026_chr12-2187537-2190115.tsv │ │ │ ├── interval_0027_chr5-30060867-30062266.tsv │ │ │ ├── interval_0028_chr6-1003683-1004493.tsv │ │ │ ├── interval_0030_chr14-29286331-29287419.tsv │ │ │ ├── interval_0031_chr7-26640756-26641574.tsv │ │ │ ├── interval_0032_chr6-4948049-4949056.tsv │ │ │ ├── interval_0033_chr9-1940281-1941248.tsv │ │ │ ├── interval_0034_chr14-19955750-19956691.tsv │ │ │ ├── interval_0035_chr6-2209392-2211073.tsv │ │ │ ├── interval_0036_chr1-1608911-1609767.tsv │ │ │ ├── interval_0037_chr11-14611139-14611909.tsv │ │ │ ├── interval_0038_chr18-19963184-19964018.tsv │ │ │ ├── interval_0039_chr24-10286328-10287069.tsv │ │ │ ├── interval_0040_chr1-28861433-28862812.tsv │ │ │ ├── interval_0041_chr1-28858118-28859215.tsv │ │ │ ├── interval_0042_chr3-16474087-16474976.tsv │ │ │ ├── interval_0043_chr23-3850204-3850968.tsv │ │ │ ├── interval_0044_chr15-29821056-29822141.tsv │ │ │ ├── interval_0045_chr13-383208-383975.tsv │ │ │ ├── interval_0046_chr8-21261846-21262796.tsv │ │ │ ├── interval_0047_chr10-1395471-1396245.tsv │ │ │ ├── interval_0048_chr23-22979232-22979976.tsv │ │ │ ├── interval_0049_chr16-27924435-27925464.tsv │ │ │ └── interval_0050_chr21-28550521-28551558.tsv │ │ ├── pycoMeth_summary_intervals.tsv │ │ ├── pycoMeth_summary_report.html │ │ └── static_plots │ │ │ ├── all_catplot.svg │ │ │ ├── all_heatmap.svg │ │ │ ├── all_ideogram.svg │ │ │ ├── all_ridgeplot.svg │ │ │ ├── all_tss_distance.svg │ │ │ ├── interval_0001_chr15-13014693-13015794_heatmap.svg │ │ │ ├── interval_0001_chr15-13014693-13015794_ridgeplot.svg │ │ │ ├── interval_0002_chr16-26220047-26221325_heatmap.svg │ │ │ ├── interval_0002_chr16-26220047-26221325_ridgeplot.svg │ │ │ ├── interval_0003_chr17-316390-318610_heatmap.svg │ │ │ ├── interval_0003_chr17-316390-318610_ridgeplot.svg │ │ │ ├── interval_0004_chr11-27686928-27688355_heatmap.svg │ │ │ ├── interval_0004_chr11-27686928-27688355_ridgeplot.svg │ │ │ ├── interval_0005_chr4-7874048-7875618_heatmap.svg │ │ │ ├── interval_0005_chr4-7874048-7875618_ridgeplot.svg │ │ │ ├── interval_0006_chr15-1565040-1565987_heatmap.svg │ │ │ ├── interval_0006_chr15-1565040-1565987_ridgeplot.svg │ │ │ ├── interval_0007_chr2-23361417-23362425_heatmap.svg │ │ │ ├── interval_0007_chr2-23361417-23362425_ridgeplot.svg │ │ │ ├── interval_0008_chr2-12169442-12171060_heatmap.svg │ │ │ ├── interval_0008_chr2-12169442-12171060_ridgeplot.svg │ │ │ ├── interval_0009_chr8-450569-451548_heatmap.svg │ │ │ ├── interval_0009_chr8-450569-451548_ridgeplot.svg │ │ │ ├── interval_0010_chr8-23224550-23225428_heatmap.svg │ │ │ ├── interval_0010_chr8-23224550-23225428_ridgeplot.svg │ │ │ ├── interval_0011_chr2-3660038-3660922_heatmap.svg │ │ │ ├── interval_0011_chr2-3660038-3660922_ridgeplot.svg │ │ │ ├── interval_0012_chr22-1816785-1817685_heatmap.svg │ │ │ ├── interval_0012_chr22-1816785-1817685_ridgeplot.svg │ │ │ ├── interval_0013_chr16-7720134-7721846_heatmap.svg │ │ │ ├── interval_0013_chr16-7720134-7721846_ridgeplot.svg │ │ │ ├── interval_0014_chr5-19638728-19639909_heatmap.svg │ │ │ ├── interval_0014_chr5-19638728-19639909_ridgeplot.svg │ │ │ ├── interval_0015_chr14-24222331-24223586_heatmap.svg │ │ │ ├── interval_0015_chr14-24222331-24223586_ridgeplot.svg │ │ │ ├── interval_0016_chr20-15042642-15043458_heatmap.svg │ │ │ ├── interval_0016_chr20-15042642-15043458_ridgeplot.svg │ │ │ ├── interval_0017_chr3-309650-310584_heatmap.svg │ │ │ ├── interval_0017_chr3-309650-310584_ridgeplot.svg │ │ │ ├── interval_0018_chr19-1948176-1949405_heatmap.svg │ │ │ ├── interval_0018_chr19-1948176-1949405_ridgeplot.svg │ │ │ ├── interval_0019_chr14-29614617-29615705_heatmap.svg │ │ │ ├── interval_0019_chr14-29614617-29615705_ridgeplot.svg │ │ │ ├── interval_0020_chr22-2405753-2407192_heatmap.svg │ │ │ ├── interval_0020_chr22-2405753-2407192_ridgeplot.svg │ │ │ ├── interval_0021_chr16-7663486-7664331_heatmap.svg │ │ │ ├── interval_0021_chr16-7663486-7664331_ridgeplot.svg │ │ │ ├── interval_0022_chr9-1939074-1940052_heatmap.svg │ │ │ ├── interval_0022_chr9-1939074-1940052_ridgeplot.svg │ │ │ ├── interval_0023_chr17-48535-49910_heatmap.svg │ │ │ ├── interval_0023_chr17-48535-49910_ridgeplot.svg │ │ │ ├── interval_0024_chr2-22706556-22707650_heatmap.svg │ │ │ ├── interval_0024_chr2-22706556-22707650_ridgeplot.svg │ │ │ ├── interval_0025_chr2-23324373-23325538_heatmap.svg │ │ │ ├── interval_0025_chr2-23324373-23325538_ridgeplot.svg │ │ │ ├── interval_0026_chr12-2187537-2190115_heatmap.svg │ │ │ ├── interval_0026_chr12-2187537-2190115_ridgeplot.svg │ │ │ ├── interval_0027_chr5-30060867-30062266_heatmap.svg │ │ │ ├── interval_0027_chr5-30060867-30062266_ridgeplot.svg │ │ │ ├── interval_0028_chr6-1003683-1004493_heatmap.svg │ │ │ ├── interval_0028_chr6-1003683-1004493_ridgeplot.svg │ │ │ ├── interval_0029_chr3-7956996-7957867_heatmap.svg │ │ │ ├── interval_0029_chr3-7956996-7957867_ridgeplot.svg │ │ │ ├── interval_0030_chr14-29286331-29287419_heatmap.svg │ │ │ ├── interval_0030_chr14-29286331-29287419_ridgeplot.svg │ │ │ ├── interval_0031_chr7-26640756-26641574_heatmap.svg │ │ │ ├── interval_0031_chr7-26640756-26641574_ridgeplot.svg │ │ │ ├── interval_0032_chr6-4948049-4949056_heatmap.svg │ │ │ ├── interval_0032_chr6-4948049-4949056_ridgeplot.svg │ │ │ ├── interval_0033_chr9-1940281-1941248_heatmap.svg │ │ │ ├── interval_0033_chr9-1940281-1941248_ridgeplot.svg │ │ │ ├── interval_0034_chr14-19955750-19956691_heatmap.svg │ │ │ ├── interval_0034_chr14-19955750-19956691_ridgeplot.svg │ │ │ ├── interval_0035_chr6-2209392-2211073_heatmap.svg │ │ │ ├── interval_0035_chr6-2209392-2211073_ridgeplot.svg │ │ │ ├── interval_0036_chr1-1608911-1609767_heatmap.svg │ │ │ ├── interval_0036_chr1-1608911-1609767_ridgeplot.svg │ │ │ ├── interval_0037_chr11-14611139-14611909_heatmap.svg │ │ │ ├── interval_0037_chr11-14611139-14611909_ridgeplot.svg │ │ │ ├── interval_0038_chr18-19963184-19964018_heatmap.svg │ │ │ ├── interval_0038_chr18-19963184-19964018_ridgeplot.svg │ │ │ ├── interval_0039_chr24-10286328-10287069_heatmap.svg │ │ │ ├── interval_0039_chr24-10286328-10287069_ridgeplot.svg │ │ │ ├── interval_0040_chr1-28861433-28862812_heatmap.svg │ │ │ ├── interval_0040_chr1-28861433-28862812_ridgeplot.svg │ │ │ ├── interval_0041_chr1-28858118-28859215_heatmap.svg │ │ │ ├── interval_0041_chr1-28858118-28859215_ridgeplot.svg │ │ │ ├── interval_0042_chr3-16474087-16474976_heatmap.svg │ │ │ ├── interval_0042_chr3-16474087-16474976_ridgeplot.svg │ │ │ ├── interval_0043_chr23-3850204-3850968_heatmap.svg │ │ │ ├── interval_0043_chr23-3850204-3850968_ridgeplot.svg │ │ │ ├── interval_0044_chr15-29821056-29822141_heatmap.svg │ │ │ ├── interval_0044_chr15-29821056-29822141_ridgeplot.svg │ │ │ ├── interval_0045_chr13-383208-383975_heatmap.svg │ │ │ ├── interval_0045_chr13-383208-383975_ridgeplot.svg │ │ │ ├── interval_0046_chr8-21261846-21262796_heatmap.svg │ │ │ ├── interval_0046_chr8-21261846-21262796_ridgeplot.svg │ │ │ ├── interval_0047_chr10-1395471-1396245_heatmap.svg │ │ │ ├── interval_0047_chr10-1395471-1396245_ridgeplot.svg │ │ │ ├── interval_0048_chr23-22979232-22979976_heatmap.svg │ │ │ ├── interval_0048_chr23-22979232-22979976_ridgeplot.svg │ │ │ ├── interval_0049_chr16-27924435-27925464_heatmap.svg │ │ │ ├── interval_0049_chr16-27924435-27925464_ridgeplot.svg │ │ │ ├── interval_0050_chr21-28550521-28551558_heatmap.svg │ │ │ └── interval_0050_chr21-28550521-28551558_ridgeplot.svg │ ├── usage.md │ └── yeast_html │ │ ├── interval_reports │ │ └── interval_0001_chrV-65380-65612.html │ │ ├── interval_tables │ │ └── interval_0001_chrV-65380-65612.tsv │ │ ├── pycoMeth_summary_intervals.tsv │ │ └── pycoMeth_summary_report.html ├── CpG_Aggregate │ ├── API_usage.ipynb │ ├── CLI_usage.ipynb │ └── usage.md ├── Interval_Aggregate │ ├── API_usage.ipynb │ ├── CLI_usage.ipynb │ └── usage.md ├── Meth_Comp │ ├── API_usage.ipynb │ ├── CLI_usage.ipynb │ └── usage.md ├── changelog.md ├── code_of_conduct.md ├── contributing.md ├── index.md ├── installation.md ├── licence.md └── pictures │ ├── CGI_Finder.png │ ├── CpG_Aggregate.png │ ├── CpG_Aggregate_2.png │ ├── CpG_Aggregate_2.svg │ ├── Interval_Aggregate.png │ ├── Interval_Aggregate_2.png │ ├── Interval_Aggregate_2.svg │ ├── Meth_Comp.png │ ├── Meth_comp.png │ ├── Meth_comp.svg │ ├── all_results_igv.png │ ├── all_results_igv_2.png │ ├── pycoMeth_HTML.gif │ ├── pycoMeth_all.png │ ├── pycoMeth_all.svg │ ├── pycoMeth_long.png │ ├── pycoMeth_long.svg │ ├── pycoMeth_package.png │ ├── pycoMeth_package.svg │ ├── pycoMeth_short.png │ └── pycoMeth_short.svg ├── meta.yaml ├── mkdocs.yml ├── pycoMeth ├── CGI_Finder.py ├── Comp_Report.py ├── CoordGen.py ├── CpG_Aggregate.py ├── FileParser.py ├── Interval_Aggregate.py ├── Meth_Comp.py ├── __init__.py ├── __main__.py ├── common.py └── templates │ ├── CpG_Interval.html.j2 │ └── CpG_summary.html.j2 └── setup.py /.gitattributes: -------------------------------------------------------------------------------- 1 | tests/* linguist-documentation 2 | docs/formatter.rb linguist-documentation=false 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | *.egg-info/ 24 | .installed.cfg 25 | *.egg 26 | MANIFEST 27 | conda_build 28 | 29 | # PyInstaller 30 | # Usually these files are written by a python script from a template 31 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 32 | *.manifest 33 | *.spec 34 | 35 | # Installer logs 36 | pip-log.txt 37 | pip-delete-this-directory.txt 38 | 39 | # Unit test / coverage reports 40 | htmlcov/ 41 | .tox/ 42 | .coverage 43 | .coverage.* 44 | .cache 45 | nosetests.xml 46 | coverage.xml 47 | *.cover 48 | .hypothesis/ 49 | .pytest_cache/ 50 | 51 | # Translations 52 | *.mo 53 | *.pot 54 | 55 | # Django stuff: 56 | *.log 57 | local_settings.py 58 | db.sqlite3 59 | 60 | # Flask stuff: 61 | instance/ 62 | .webassets-cache 63 | 64 | # Scrapy stuff: 65 | .scrapy 66 | 67 | # Sphinx documentation 68 | docs/_build/ 69 | 70 | # PyBuilder 71 | target/ 72 | 73 | # Jupyter Notebook 74 | .ipynb_checkpoints 75 | 76 | # pyenv 77 | .python-version 78 | 79 | # celery beat schedule file 80 | celerybeat-schedule 81 | 82 | # SageMath parsed files 83 | *.sage.py 84 | 85 | # Environments 86 | .env 87 | .venv 88 | env/ 89 | venv/ 90 | ENV/ 91 | env.bak/ 92 | venv.bak/ 93 | 94 | # Spyder project settings 95 | .spyderproject 96 | .spyproject 97 | 98 | # Rope project settings 99 | .ropeproject 100 | 101 | # mkdocs documentation 102 | /site 103 | 104 | # mypy 105 | .mypy_cache/ 106 | tests/ 107 | 108 | # demo_results 109 | docs/*/results/ 110 | docs/*/data/ 111 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | dist: xenial 2 | language: python 3 | python: 3.6 4 | branches: 5 | only: 6 | - master 7 | - dev 8 | 9 | install: 10 | # Install other pip dependencies 11 | - pip install nbconvert requests jinja2 mkdocs mkdocs-material pygments pymdown-extensions mkdocs-exclude 12 | # Install this one after or it raises an error 13 | - pip install mknotebooks 14 | 15 | script: true 16 | 17 | before_deploy: 18 | # Prebuild mkdocs site documentation 19 | - mkdocs build --verbose --clean 20 | 21 | deploy: 22 | # Deploy mkdoc documentation to github page 23 | - provider: pages 24 | skip_cleanup: true 25 | target_branch: gh-pages-test 26 | github_token: "$GH_TOKEN" 27 | local_dir: site 28 | on: 29 | branch: dev 30 | 31 | - provider: pages 32 | skip_cleanup: true 33 | github_token: "$GH_TOKEN" 34 | local_dir: site 35 | on: 36 | branch: master 37 | 38 | # Deploy package to pypy 39 | - provider: pypi 40 | user: aleg 41 | password: "$PYPI_PW" 42 | server: https://test.pypi.org/legacy/ 43 | on: 44 | branch: dev 45 | 46 | - provider: pypi 47 | user: aleg 48 | password: "$PYPI_PW" 49 | on: 50 | branch: master 51 | 52 | # Deploy to Anaconda 53 | - provider: script 54 | skip_cleanup: true 55 | script: bash ./deploy_anaconda.sh $ANACONDA_DEV_TOKEN 56 | on: 57 | branch: dev 58 | 59 | - provider: script 60 | skip_cleanup: true 61 | script: bash ./deploy_anaconda.sh $ANACONDA_TOKEN 62 | on: 63 | branch: master 64 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | # pycoMeth Changelog 2 | 3 | ### 09/10/2019 v-0.1.0 4 | 5 | * Deep refactoring of Freq_meth_calculate to Aggregate 6 | * Major doc update including doc folders reorganisation 7 | * Implement autodoc from docstring 8 | * Fix and test CLI 9 | 10 | ### 01/04/2020 v-0.4.0 11 | 12 | * General improvement of logging message output 13 | * Implement fancy color logger 14 | * Add position tracking within intervals 15 | * Add Comp_Report module to generate HTML reports of significant candidates 16 | 17 | ### 15/01/2020 v-0.4.5 18 | 19 | * Add tabular text reports to Comp_report 20 | * Add (default) option to write out all the intervals in Meth_Comp with reasons why excluded or included in DM analysis 21 | * Improve Comp_report summary table and include new fields from Meth_Comp 22 | * Tidy output folder structure for reports generated by meth_report 23 | * Add Chromosome ideogram plot to summary report 24 | * A fasta reference is now required to run Comp_Report 25 | 26 | ### 09/07/2020 v-0.4.8 27 | 28 | * Speed improvement to Comp_report 29 | * Add interactive API to Comp_report 30 | * Add ability to export static plots using orca 31 | 32 | ### 16/07/2020 v-0.4.14 33 | 34 | * Switch from orca to kaleido for static export 35 | * Export summary of intervals in table file for all intervals and not just for top hits 36 | * Add new plot for distance between CpG islands and closest tss 37 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Contributor Covenant Code of Conduct 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open and welcoming environment, we as 6 | contributors and maintainers pledge to making participation in our project and 7 | our community a harassment-free experience for everyone, regardless of age, body 8 | size, disability, ethnicity, sex characteristics, gender identity and expression, 9 | level of experience, education, socio-economic status, nationality, personal 10 | appearance, race, religion, or sexual identity and orientation. 11 | 12 | ## Our Standards 13 | 14 | Examples of behavior that contributes to creating a positive environment 15 | include: 16 | 17 | * Using welcoming and inclusive language 18 | * Being respectful of differing viewpoints and experiences 19 | * Gracefully accepting constructive criticism 20 | * Focusing on what is best for the community 21 | * Showing empathy towards other community members 22 | 23 | Examples of unacceptable behavior by participants include: 24 | 25 | * The use of sexualized language or imagery and unwelcome sexual attention or 26 | advances 27 | * Trolling, insulting/derogatory comments, and personal or political attacks 28 | * Public or private harassment 29 | * Publishing others' private information, such as a physical or electronic 30 | address, without explicit permission 31 | * Other conduct which could reasonably be considered inappropriate in a 32 | professional setting 33 | 34 | ## Our Responsibilities 35 | 36 | Project maintainers are responsible for clarifying the standards of acceptable 37 | behavior and are expected to take appropriate and fair corrective action in 38 | response to any instances of unacceptable behavior. 39 | 40 | Project maintainers have the right and responsibility to remove, edit, or 41 | reject comments, commits, code, wiki edits, issues, and other contributions 42 | that are not aligned to this Code of Conduct, or to ban temporarily or 43 | permanently any contributor for other behaviors that they deem inappropriate, 44 | threatening, offensive, or harmful. 45 | 46 | ## Scope 47 | 48 | This Code of Conduct applies both within project spaces and in public spaces 49 | when an individual is representing the project or its community. Examples of 50 | representing a project or community include using an official project e-mail 51 | address, posting via an official social media account, or acting as an appointed 52 | representative at an online or offline event. Representation of a project may be 53 | further defined and clarified by project maintainers. 54 | 55 | ## Enforcement 56 | 57 | Instances of abusive, harassing, or otherwise unacceptable behavior may be 58 | reported by contacting the project team at aleg@ebi.ac.uk. All 59 | complaints will be reviewed and investigated and will result in a response that 60 | is deemed necessary and appropriate to the circumstances. The project team is 61 | obligated to maintain confidentiality with regard to the reporter of an incident. 62 | Further details of specific enforcement policies may be posted separately. 63 | 64 | Project maintainers who do not follow or enforce the Code of Conduct in good 65 | faith may face temporary or permanent repercussions as determined by other 66 | members of the project's leadership. 67 | 68 | ## Attribution 69 | 70 | This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, 71 | available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html 72 | 73 | [homepage]: https://www.contributor-covenant.org 74 | 75 | For answers to common questions about this code of conduct, see 76 | https://www.contributor-covenant.org/faq 77 | -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing to pycoMeth 2 | 3 | First of all, thanks for considering contributing to `pycoMeth`! 👍 It's people like you that make it rewarding for us to work on `pycoMeth`. 4 | 5 | `pycoMeth` is an open source project, maintained by publicly funded academic researchers. 6 | 7 | [repo]: https://github.com/a-slide/pycoMeth 8 | [issues]: https://github.com/a-slide/pycoMeth/issues 9 | [new_issue]: https://github.com/a-slide/pycoMeth/issues/new 10 | [code_of_conduct]: https://github.com/a-slide/pycoMeth/blob/master/docs/code_of_conduct.md 11 | 12 | ## Code of conduct 13 | 14 | Please note that this project is released with a [Contributor Code of Conduct][code_of_conduct]. By participating in this project you agree to abide by its terms. 15 | 16 | ## How you can contribute 17 | 18 | There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this [Open Source Guide](https://opensource.guide/how-to-contribute/). 19 | 20 | ### Share the love ❤️ 21 | 22 | Think `pycoMeth` is useful? Let others discover it, by telling them in person, via Twitter or a blog post. 23 | 24 | Using `pycoMeth` for a paper you are writing? Please cite it. 25 | 26 | ### Ask a question ⁉️ 27 | 28 | Using `pycoMeth` and got stuck? Browse the documentation to see if you can find a solution. 29 | 30 | Still stuck? Post your question as an [issue on GitHub][new_issue]. 31 | 32 | While we cannot offer user support, we'll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs. 33 | 34 | 35 | ### Propose an idea 💡 36 | 37 | Have an idea for a new `pycoMeth` feature? Take a look at the [issue list][issues] to see if it isn't included or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. While we can't promise to implement your idea, it helps to: 38 | 39 | * Explain in detail how it would work. 40 | * Keep the scope as narrow as possible. 41 | 42 | See below if you want to contribute code for your idea as well. 43 | 44 | ### Report a bug 🐛 45 | 46 | Using `pycoMeth` and discovered a bug? That's annoying! Don't let others have the same experience and report it as an [issue on GitHub][new_issue] so we can fix it. A good bug report makes it easier for us to do so, so please include: 47 | 48 | * Your operating system name and version (e.g. Mac OS 10.13.6). 49 | * Any details about your local setup that might be helpful in troubleshooting. 50 | * Detailed steps to reproduce the bug. 51 | 52 | ### Improve the documentation 📖 53 | 54 | Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome! 55 | 56 | 1. Fork [pycoMeth][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/). 57 | 2. Edit the README.md file and submit a pull request. We will review your changes and include the fix in the next release. 58 | 59 | ### Contribute code 📝 60 | 61 | Care to fix bugs or implement new functionality for `pycoMeth`? Awesome! 👏 Have a look at the [issue list][issues] and leave a comment on the things you want to work on. See also the development guidelines below. 62 | 63 | ## Development guidelines 64 | 65 | We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development and the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style Guide for Python Code. 66 | 67 | 1. Fork [pycoMeth][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/). 68 | 69 | 2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`. 70 | 71 | 3. Make your changes and test the modified code. 72 | 73 | 4. Commit and push your changes. 74 | 75 | 5. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request). 76 | 77 | 78 | --- 79 | 80 | This file was adapted from a template created by [peterdesmet](https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c). 81 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Deprecation notice 2 | 3 | This fork is now deprecated. 4 | 5 | PycoMeth is now maintened and developped by [Rene Snajder](https://github.com/snajder-r) at the following URL: 6 | 7 | **https://github.com/snajder-r/pycoMeth** 8 | -------------------------------------------------------------------------------- /deploy_anaconda.sh: -------------------------------------------------------------------------------- 1 | #!bash 2 | # -*- coding: utf-8 -*- 3 | 4 | set -e 5 | 6 | echo "Set up conda package manager" 7 | wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh --quiet 8 | bash miniconda.sh -b -p $HOME/miniconda 9 | export PATH="$HOME/miniconda/bin:$PATH" 10 | hash -r 11 | conda config --set always_yes yes --set changeps1 no --set anaconda_upload no 12 | conda update -q conda 13 | 14 | echo "Install packages needed for package build and upload" 15 | conda install -q python=3.7 conda-build anaconda-client ripgrep conda-verify 16 | 17 | echo "compile package from setup.py" 18 | python setup.py sdist 19 | 20 | echo "Build noarch package..." 21 | conda-build meta.yaml --python 3.7 --numpy 1.1 --output-folder conda_build -c bioconda -c conda-forge -c plotly --no-include-recipe 22 | 23 | echo "Deploying to Anaconda.org..." 24 | anaconda -v -t $1 upload conda_build/**/*.tar.bz2 25 | 26 | echo "Successfully deployed to Anaconda.org." 27 | exit 0 28 | -------------------------------------------------------------------------------- /docs/CGI_Finder/usage.md: -------------------------------------------------------------------------------- 1 | # CGI_Finder usage 2 | 3 | **Simple method to find putative CpG islands in DNA sequences by using a sliding window and merging overlapping windows satisfying the CpG island definition. Results can be saved in bed and tsv format.** 4 | 5 | ## Example usage 6 | 7 | * [Python API usage](https://a-slide.github.io/pycoMeth/CGI_Finder/API_usage/) 8 | * [Shell CLI usage](https://a-slide.github.io/pycoMeth/CGI_Finder/CLI_usage/) 9 | 10 | ## Input file 11 | 12 | ### Reference FASTA file 13 | 14 | FASTA reference file containing sequences in which CpG islands needs to be found. 15 | 16 | ## Output files 17 | 18 | ### Tabulated TSV file 19 | 20 | This tabulated file contains the following fields for each CpG island found: 21 | 22 | * chromosome / start / end : Genomic coordinates 23 | * length: Length of the interval 24 | * num_CpG: Number of CpGs found 25 | * CG_freq: G+C nucleotide frequency 26 | * obs_exp_freq: Observed versus expected CpG frequency 27 | 28 | ### BED file 29 | 30 | Minimal standard genomic [BED3](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) format listing the coordinates of putative CpG islands. 31 | 32 | The picture below shows the putative CpG islands found (grey boxes) in an example sequence, overlaid with C+G frequency and observed/expected CpG frequency 33 | 34 | ![Example](../pictures/CGI_Finder.png) 35 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0003_chr16-54936192-54939415.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000558156 sg00000259725 ac106738.2-202 16 54938031 54938671 - lnc_RNA lncrna 3 | 0 enst00000559802 sg00000259725 ac106738.2-201 16 54937786 54938671 - lnc_RNA lncrna 4 | -1279 enst00000560487 sg00000259711 ac106738.1-201 16 54934913 54954665 + lnc_RNA lncrna 5 | -4120 enst00000558597 sg00000176842 irx5-203 16 54932072 54934069 + lnc_RNA retained_intron 6 | -4993 enst00000320990 sg00000176842 irx5-201 16 54931199 54934485 + mRNA protein_coding 7 | -4993 enst00000620085 sg00000176842 irx5-205 16 54931199 54933960 + mRNA protein_coding 8 | -4993 enst00000560154 sg00000176842 irx5-204 16 54931199 54933960 + mRNA protein_coding 9 | -5327 enst00000394636 sg00000176842 irx5-202 16 54930865 54934485 + mRNA protein_coding 10 | -7003 enst00000660344 sg00000245694 crnde-220 16 54917956 54929189 - lnc_RNA lncrna 11 | -7043 enst00000560208 sg00000245694 crnde-209 16 54924859 54929149 - lnc_RNA lncrna 12 | -7306 enst00000558952 sg00000245694 crnde-205 16 54919157 54928886 - lnc_RNA lncrna 13 | -7334 enst00000668556 sg00000245694 crnde-224 16 54916492 54928858 - lnc_RNA lncrna 14 | -7345 enst00000557792 sg00000245694 crnde-203 16 54918967 54928847 - lnc_RNA lncrna 15 | -7349 enst00000661493 sg00000245694 crnde-222 16 54852903 54928843 - lnc_RNA lncrna 16 | -7354 enst00000502066 sg00000245694 crnde-202 16 54917968 54928838 - lnc_RNA lncrna 17 | -7365 enst00000559598 sg00000245694 crnde-207 16 54917970 54928827 - lnc_RNA lncrna 18 | -7380 enst00000560912 sg00000245694 crnde-210 16 54919173 54928812 - lnc_RNA lncrna 19 | -7476 enst00000559432 sg00000245694 crnde-206 16 54919066 54928716 - lnc_RNA lncrna 20 | -7614 enst00000501177 sg00000245694 crnde-201 16 54918863 54928578 - lnc_RNA lncrna 21 | -7898 enst00000655114 sg00000245694 crnde-216 16 54919047 54928294 - lnc_RNA lncrna 22 | -8002 enst00000657142 sg00000245694 crnde-217 16 54918942 54928190 - lnc_RNA lncrna 23 | -8466 enst00000661312 sg00000245694 crnde-221 16 54918917 54927726 - lnc_RNA lncrna 24 | -11048 enst00000613942 sg00000245694 crnde-212 16 54851640 54925144 - lnc_RNA lncrna 25 | -12304 enst00000558031 sg00000245694 crnde-204 16 54919011 54923888 - lnc_RNA lncrna 26 | -15576 enst00000560029 sg00000245694 crnde-208 16 54918870 54920616 - lnc_RNA lncrna 27 | -62022 enst00000658082 sg00000245694 crnde-218 16 54851643 54874170 - lnc_RNA lncrna 28 | -62024 enst00000637011 sg00000245694 crnde-214 16 54847247 54874168 - lnc_RNA lncrna 29 | 68567 enst00000568888 sg00000260147 mtnd5p34-201 16 55007982 55008306 + pseudogenic_transcript processed_pseudogene 30 | -87873 enst00000659020 sg00000245694 crnde-219 16 54847247 54848319 - lnc_RNA lncrna 31 | -87882 enst00000654070 sg00000245694 crnde-215 16 54847175 54848310 - lnc_RNA lncrna 32 | -87914 enst00000635991 sg00000245694 crnde-213 16 54845189 54848278 - lnc_RNA lncrna 33 | -87943 enst00000667913 sg00000245694 crnde-223 16 54847247 54848249 - lnc_RNA lncrna 34 | -87959 enst00000561591 sg00000245694 crnde-211 16 54847247 54848233 - lnc_RNA lncrna 35 | -88876 enst00000659355 sg00000286357 ac106742.1-201 16 54847316 54854991 + lnc_RNA lncrna 36 | 109903 enst00000650608 sg00000285775 ac109136.1-201 16 55045700 55049318 - lnc_RNA lncrna 37 | -278530 enst00000637560 sg00000283258 ac007491.1-201 16 54628963 54657662 - lnc_RNA lncrna 38 | -301855 enst00000637961 sg00000283258 ac007491.1-202 16 54631754 54634337 - lnc_RNA lncrna 39 | 352260 enst00000470547 sg00000239555 rn7sl841p-201 16 55291379 55291675 - ncRNA misc_rna 40 | -377092 enst00000637822 sg00000283304 linc02183-201 16 54542808 54559100 - lnc_RNA lncrna 41 | 383271 enst00000637882 sg00000283423 ac109462.3-201 16 55321575 55322686 - lnc_RNA lncrna 42 | 384345 enst00000290552 sg00000159387 irx6-201 16 55323760 55330760 + mRNA protein_coding 43 | 386385 enst00000558315 sg00000159387 irx6-202 16 55325800 55327796 + lnc_RNA processed_transcript 44 | 392940 enst00000573934 sg00000263207 ac109462.2-201 16 55332355 55332967 + lnc_RNA lncrna 45 | 394173 enst00000558730 sg00000259283 ac109462.1-201 16 55259969 55333588 - lnc_RNA lncrna 46 | 413673 enst00000491087 sg00000240760 rpl31p56-201 16 55352721 55353088 - pseudogenic_transcript processed_pseudogene 47 | -444796 enst00000660981 sg00000286845 ac007343.1-201 16 54490281 54491396 - lnc_RNA lncrna 48 | 450285 enst00000570308 sg00000087245 mmp2-208 16 55389700 55506237 + mRNA protein_coding 49 | 486715 enst00000611626 sg00000274508 ac007336.2-201 16 55425574 55426130 - lnc_RNA lncrna 50 | 488536 enst00000620495 sg00000260135 mmp2-as1-203 16 55426797 55427951 - lnc_RNA lncrna 51 | 489223 enst00000664911 sg00000260135 mmp2-as1-204 16 55426803 55428638 - lnc_RNA lncrna 52 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0009_chr17-61403712-61405954.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2768 enst00000586986 sg00000121068 tbx2-204 17 61408722 61409466 + lnc_RNA processed_transcript 3 | -3347 enst00000477081 sg00000121068 tbx2-203 17 61400365 61409124 + lnc_RNA retained_intron 4 | -3469 enst00000585765 sg00000267131 ac005746.2-201 17 61361668 61400243 - lnc_RNA lncrna 5 | -3802 enst00000419047 sg00000121068 tbx2-202 17 61399910 61409466 + mRNA nonsense_mediated_decay 6 | -3869 enst00000240328 sg00000121068 tbx2-201 17 61399843 61409466 + mRNA protein_coding 7 | -4106 enst00000590421 sg00000267280 tbx2-as1-203 17 61393457 61399606 - lnc_RNA lncrna 8 | -4124 enst00000591313 sg00000267280 tbx2-as1-204 17 61393458 61399588 - lnc_RNA lncrna 9 | -4342 enst00000589814 sg00000267280 tbx2-as1-202 17 61393458 61399370 - lnc_RNA lncrna 10 | 5601 enst00000592009 sg00000267280 tbx2-as1-205 17 61393458 61411555 - lnc_RNA lncrna 11 | 5797 enst00000623772 sg00000187013 c17orf82-201 17 61411751 61413280 + lnc_RNA lncrna 12 | -8265 enst00000586706 sg00000267280 tbx2-as1-201 17 61393458 61395447 - lnc_RNA lncrna 13 | -9650 enst00000592377 sg00000267280 tbx2-as1-206 17 61393456 61394062 - lnc_RNA lncrna 14 | -15436 enst00000588720 sg00000141376 bcas3-220 17 61388276 61392831 + lnc_RNA retained_intron 15 | -20311 enst00000585495 sg00000266934 ac005746.1-202 17 61383401 61384680 + lnc_RNA lncrna 16 | -20927 enst00000589244 sg00000266934 ac005746.1-201 17 61382785 61383555 + lnc_RNA lncrna 17 | -25882 enst00000587872 sg00000141376 bcas3-214 17 61377830 61380572 + lnc_RNA retained_intron 18 | 46450 enst00000589003 sg00000121075 tbx4-203 17 61452404 61478740 + mRNA protein_coding 19 | 46468 enst00000644296 sg00000121075 tbx4-208 17 61452422 61485110 + mRNA protein_coding 20 | -48557 enst00000614751 sg00000273982 ac005746.3-201 17 61354763 61355155 - lnc_RNA lncrna 21 | 50492 enst00000240335 sg00000121075 tbx4-201 17 61456446 61484303 + mRNA protein_coding 22 | 50510 enst00000642491 sg00000121075 tbx4-207 17 61456464 61483997 + mRNA protein_coding 23 | 57430 enst00000592766 sg00000267137 ac005901.1-201 17 61460224 61463384 - lnc_RNA lncrna 24 | 58260 enst00000593249 sg00000121075 tbx4-206 17 61464214 61478789 + lnc_RNA processed_transcript 25 | 59839 enst00000590174 sg00000121075 tbx4-205 17 61465793 61480275 + lnc_RNA retained_intron 26 | 72397 enst00000589449 sg00000121075 tbx4-204 17 61478351 61483370 + lnc_RNA processed_transcript 27 | 72409 enst00000586874 sg00000121075 tbx4-202 17 61478363 61481346 + lnc_RNA processed_transcript 28 | -158452 enst00000588569 sg00000141376 bcas3-219 17 61245260 61392273 + lnc_RNA processed_transcript 29 | -158496 enst00000592702 sg00000141376 bcas3-229 17 61245216 61392831 + lnc_RNA processed_transcript 30 | 185265 enst00000521764 sg00000253506 naca2-201 17 61590421 61591219 - mRNA protein_coding 31 | -244350 enst00000587294 sg00000141376 bcas3-213 17 61159362 61392182 + lnc_RNA processed_transcript 32 | -246256 enst00000585812 sg00000141376 bcas3-205 17 61157456 61392831 + lnc_RNA processed_transcript 33 | -267743 enst00000666957 sg00000286997 ac005856.1-201 17 61119095 61135969 - lnc_RNA lncrna 34 | -319207 enst00000588008 sg00000141376 bcas3-215 17 61084505 61087498 + lnc_RNA processed_transcript 35 | -325271 enst00000587002 sg00000141376 bcas3-211 17 61078441 61368410 + mRNA protein_coding 36 | -333356 enst00000593107 sg00000267449 ac005884.2-201 17 61069856 61070356 - lnc_RNA lncrna 37 | -333590 enst00000588604 sg00000267207 ac005884.1-201 17 61034636 61070122 - lnc_RNA lncrna 38 | -333841 enst00000437246 sg00000227694 rpl23ap74-201 17 61069871 61070341 + pseudogenic_transcript processed_pseudogene 39 | 370526 enst00000584322 sg00000136492 brip1-206 17 61739057 61776480 - mRNA protein_coding 40 | 374323 enst00000583837 sg00000136492 brip1-205 17 61775878 61780277 - lnc_RNA processed_transcript 41 | -386748 enst00000592827 sg00000141376 bcas3-230 17 61016964 61074988 + lnc_RNA processed_transcript 42 | -386750 enst00000585979 sg00000141376 bcas3-206 17 61016962 61368342 + lnc_RNA processed_transcript 43 | 387719 enst00000579028 sg00000136492 brip1-204 17 61776401 61793673 - mRNA nonsense_mediated_decay 44 | -401155 enst00000587037 sg00000141376 bcas3-212 17 61002557 61037903 + lnc_RNA processed_transcript 45 | -416855 enst00000590352 sg00000141376 bcas3-225 17 60986857 61015785 + lnc_RNA processed_transcript 46 | 455585 enst00000577598 sg00000136492 brip1-202 17 61684772 61861539 - mRNA protein_coding 47 | 457390 enst00000577913 sg00000136492 brip1-203 17 61857228 61863344 - mRNA protein_coding 48 | 457574 enst00000259008 sg00000136492 brip1-201 17 61679139 61863528 - mRNA protein_coding 49 | 468228 enst00000365491 sg00000202361 ac060798.1-201 17 61874084 61874182 - ncRNA misc_rna 50 | 479051 enst00000583822 sg00000108506 ints2-205 17 61872023 61885005 - lnc_RNA retained_intron 51 | 479336 enst00000584967 sg00000108506 ints2-206 17 61877981 61885290 - lnc_RNA retained_intron 52 | 488232 enst00000578805 sg00000108506 ints2-203 17 61891577 61894186 - lnc_RNA retained_intron 53 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0010_chr8-140097670-140099673.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 870 enst00000631594 sg00000282164 peg13-201 8 140094894 140100543 - lnc_RNA lncrna 3 | -15517 enst00000523777 sg00000167632 trappc9-214 8 139732162 140082153 - lnc_RNA processed_transcript 4 | -57914 enst00000617244 sg00000274064 ac040978.1-201 8 140039756 140041037 + pseudogenic_transcript processed_pseudogene 5 | -89079 enst00000524162 sg00000167632 trappc9-215 8 139732093 140008591 - lnc_RNA processed_transcript 6 | 138820 enst00000517667 sg00000167632 trappc9-203 8 139988740 140238493 - lnc_RNA processed_transcript 7 | 163057 enst00000518839 sg00000167632 trappc9-205 8 140215910 140262730 - lnc_RNA processed_transcript 8 | 163058 enst00000520532 sg00000167632 trappc9-207 8 139988823 140262731 - lnc_RNA processed_transcript 9 | -166498 enst00000507535 sg00000250733 c8orf17-201 8 139931172 139933942 + unconfirmed_transcript tec 10 | -166498 enst00000625034 sg00000250733 c8orf17-202 8 139931172 139933946 + unconfirmed_transcript tec 11 | 176080 enst00000634178 sg00000167632 trappc9-216 8 140252571 140275753 - mRNA protein_coding 12 | -182871 enst00000521883 sg00000253574 ac021744.1-202 8 139914799 139916620 + lnc_RNA lncrna 13 | -186432 enst00000518354 sg00000253574 ac021744.1-201 8 139911238 139916620 + lnc_RNA lncrna 14 | -188912 enst00000519482 sg00000167632 trappc9-206 8 139731044 139908758 - lnc_RNA processed_transcript 15 | -188975 enst00000518723 sg00000167632 trappc9-204 8 139904432 139908695 - lnc_RNA retained_intron 16 | 191578 enst00000521667 sg00000167632 trappc9-210 8 139730892 140291251 - lnc_RNA retained_intron 17 | 203162 enst00000521167 sg00000167632 trappc9-209 8 140283987 140302835 - lnc_RNA processed_transcript 18 | -216375 enst00000522504 sg00000167632 trappc9-213 8 139730996 139881295 - lnc_RNA processed_transcript 19 | -291437 enst00000521700 sg00000167632 trappc9-211 8 139731006 139806233 - lnc_RNA processed_transcript 20 | 335524 enst00000521944 sg00000167632 trappc9-212 8 140405293 140435197 - lnc_RNA retained_intron 21 | 351257 enst00000520857 sg00000167632 trappc9-208 8 139730345 140450930 - mRNA protein_coding 22 | 358071 enst00000438773 sg00000167632 trappc9-202 8 139730343 140457744 - mRNA protein_coding 23 | 358906 enst00000389328 sg00000167632 trappc9-201 8 139730343 140458579 - mRNA protein_coding 24 | 358906 enst00000648948 sg00000167632 trappc9-217 8 139727725 140458579 - mRNA protein_coding 25 | -393561 enst00000648164 sg00000169427 kcnk9-208 8 139617121 139704109 - mRNA protein_coding 26 | -394547 enst00000520439 sg00000169427 kcnk9-203 8 139617121 139703123 - mRNA protein_coding 27 | -394577 enst00000650269 sg00000169427 kcnk9-212 8 139601097 139703093 - mRNA protein_coding 28 | -394629 enst00000522317 sg00000169427 kcnk9-204 8 139600838 139703041 - mRNA nonsense_mediated_decay 29 | -394672 enst00000303015 sg00000169427 kcnk9-201 8 139612561 139702998 - mRNA protein_coding 30 | -394714 enst00000649473 sg00000169427 kcnk9-210 8 139600839 139702956 - mRNA nonsense_mediated_decay 31 | 408370 enst00000564464 sg00000259891 ac107375.1-201 8 140505813 140508043 - lnc_RNA lncrna 32 | 411638 enst00000519533 sg00000104472 chrac1-203 8 140511311 140516467 + mRNA protein_coding 33 | 411649 enst00000220913 sg00000104472 chrac1-201 8 140511322 140517154 + mRNA protein_coding 34 | 412245 enst00000518971 sg00000104472 chrac1-202 8 140511918 140515185 + mRNA protein_coding 35 | 412309 enst00000519618 sg00000104472 chrac1-204 8 140511982 140515765 + mRNA protein_coding 36 | 414621 enst00000523569 sg00000104472 chrac1-205 8 140514294 140515541 + lnc_RNA retained_intron 37 | 433033 enst00000520628 sg00000123908 ago2-207 8 140532094 140532706 - lnc_RNA processed_transcript 38 | 439776 enst00000519347 sg00000123908 ago2-204 8 140535391 140539449 - lnc_RNA retained_intron 39 | 441784 enst00000520412 sg00000123908 ago2-206 8 140532533 140541457 - lnc_RNA retained_intron 40 | -443320 enst00000523477 sg00000169427 kcnk9-205 8 139600845 139654350 - lnc_RNA processed_transcript 41 | -443340 enst00000647605 sg00000169427 kcnk9-207 8 139617159 139654330 - mRNA protein_coding 42 | -443340 enst00000649696 sg00000169427 kcnk9-211 8 139600845 139654330 - mRNA nonsense_mediated_decay 43 | 456565 enst00000521325 sg00000123908 ago2-208 8 140555408 140556238 - lnc_RNA retained_intron 44 | -463809 enst00000648481 sg00000169427 kcnk9-209 8 139617206 139633861 - lnc_RNA processed_transcript 45 | 473139 enst00000624190 sg00000279766 ac067931.1-201 8 140572142 140572812 - unconfirmed_transcript tec 46 | -481623 enst00000519923 sg00000169427 kcnk9-202 8 139612326 139616047 - lnc_RNA processed_transcript 47 | 492011 enst00000624905 sg00000280326 ac067931.2-201 8 140591684 140593201 + unconfirmed_transcript tec 48 | -495606 enst00000523653 sg00000169427 kcnk9-206 8 139601078 139602064 - lnc_RNA processed_transcript 49 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0017_chr5-2748080-2750204.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 1458 enst00000382611 sg00000170561 irx2-202 5 2745845 2751662 - mRNA protein_coding 3 | 1473 enst00000302057 sg00000170561 irx2-201 5 2746165 2751677 - mRNA protein_coding 4 | 1927 enst00000649739 sg00000186493 c5orf38-209 5 2752131 2755081 + lnc_RNA processed_transcript 5 | 1944 enst00000647681 sg00000186493 c5orf38-208 5 2752148 2755397 + lnc_RNA processed_transcript 6 | 1944 enst00000334000 sg00000186493 c5orf38-201 5 2752148 2755397 + mRNA protein_coding 7 | 2024 enst00000650439 sg00000186493 c5orf38-210 5 2752228 2755081 + lnc_RNA processed_transcript 8 | 2024 enst00000503940 sg00000186493 c5orf38-204 5 2752228 2755081 + lnc_RNA processed_transcript 9 | 2024 enst00000505106 sg00000186493 c5orf38-205 5 2752228 2755081 + lnc_RNA processed_transcript 10 | 2042 enst00000515640 sg00000186493 c5orf38-207 5 2752246 2754373 + lnc_RNA processed_transcript 11 | 2061 enst00000505778 sg00000186493 c5orf38-206 5 2752265 2753359 + mRNA protein_coding 12 | 2061 enst00000457752 sg00000186493 c5orf38-203 5 2752265 2755041 + mRNA protein_coding 13 | 2061 enst00000397835 sg00000186493 c5orf38-202 5 2752265 2755376 + lnc_RNA processed_transcript 14 | -10321 enst00000560688 sg00000259757 ac091891.1-201 5 2736662 2737759 - lnc_RNA lncrna 15 | -35489 enst00000626215 sg00000281560 lsinct5-201 5 2712591 2715237 + lnc_RNA lncrna 16 | 38345 enst00000510731 sg00000249541 ac116359.1-201 5 2787451 2788549 - pseudogenic_transcript processed_pseudogene 17 | 84935 enst00000509745 sg00000248137 ac094105.1-201 5 2831021 2835139 - lnc_RNA lncrna 18 | 171292 enst00000652017 sg00000248736 ac094105.2-201 5 2921496 2967621 + lnc_RNA lncrna 19 | 183553 enst00000664294 sg00000248736 ac094105.2-203 5 2933757 2965538 + lnc_RNA lncrna 20 | 184950 enst00000515086 sg00000248736 ac094105.2-202 5 2935154 2967955 + lnc_RNA lncrna 21 | 427631 enst00000505396 sg00000249808 ac091832.1-201 5 3177835 3181232 + lnc_RNA lncrna 22 | 427659 enst00000652864 sg00000249808 ac091832.1-202 5 3177863 3181487 + lnc_RNA lncrna 23 | -486221 enst00000610958 sg00000275733 ac092266.1-201 5 2261859 2262023 + pseudogenic_transcript processed_pseudogene 24 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0018_chr2-66445077-66447024.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000475239 sg00000143995 meis1-208 2 66445193 66567500 + lnc_RNA processed_transcript 3 | -856 enst00000666153 sg00000230749 meis1-as2-203 2 66441650 66444221 - lnc_RNA lncrna 4 | -2112 enst00000606455 sg00000143995 meis1-217 2 66442965 66568714 + lnc_RNA processed_transcript 5 | -2302 enst00000498705 sg00000143995 meis1-214 2 66442775 66512294 + lnc_RNA retained_intron 6 | -3241 enst00000454595 sg00000230749 meis1-as2-202 2 66439443 66441836 - lnc_RNA lncrna 7 | -4370 enst00000466811 sg00000143995 meis1-207 2 66440707 66454735 + lnc_RNA processed_transcript 8 | -4399 enst00000437869 sg00000143995 meis1-205 2 66440678 66464220 + mRNA protein_coding 9 | -4765 enst00000439433 sg00000230749 meis1-as2-201 2 66439088 66440312 - lnc_RNA lncrna 10 | -4980 enst00000409622 sg00000143995 meis1-204 2 66440097 66512191 + lnc_RNA processed_transcript 11 | -5756 enst00000495021 sg00000143995 meis1-212 2 66439321 66572759 + mRNA protein_coding 12 | -7684 enst00000398506 sg00000143995 meis1-202 2 66437393 66573329 + mRNA protein_coding 13 | -8160 enst00000490726 sg00000143995 meis1-210 2 66436917 66441440 + lnc_RNA processed_transcript 14 | -9519 enst00000488550 sg00000143995 meis1-209 2 66435558 66572454 + mRNA protein_coding 15 | -9908 enst00000491706 sg00000143995 meis1-211 2 66435169 66443772 + lnc_RNA retained_intron 16 | -9944 enst00000560281 sg00000143995 meis1-216 2 66435133 66568536 + mRNA protein_coding 17 | -9952 enst00000272369 sg00000143995 meis1-201 2 66435125 66573869 + mRNA protein_coding 18 | -11607 enst00000454167 sg00000226819 meis1-as3-201 2 66426735 66433470 - lnc_RNA lncrna 19 | -11625 enst00000496248 sg00000143995 meis1-213 2 66433452 66439967 + lnc_RNA processed_transcript 20 | 14774 enst00000409517 sg00000143995 meis1-203 2 66461798 66572454 + lnc_RNA processed_transcript 21 | 49002 enst00000542964 sg00000143995 meis1-215 2 66496026 66571251 + lnc_RNA processed_transcript 22 | -61771 enst00000428647 sg00000232164 linc01873-201 2 66383306 66392450 + lnc_RNA lncrna 23 | 61903 enst00000450027 sg00000143995 meis1-206 2 66508927 66568745 + lnc_RNA processed_transcript 24 | -86749 enst00000577635 sg00000264525 mir4778-201 2 66358249 66358328 - miRNA mirna 25 | -117716 enst00000449673 sg00000225815 ac092669.1-202 2 66327361 66328984 + lnc_RNA lncrna 26 | -117728 enst00000412313 sg00000225815 ac092669.1-201 2 66327349 66328643 + lnc_RNA lncrna 27 | 127006 enst00000433396 sg00000232046 linc01798-204 2 66574030 66695505 + lnc_RNA lncrna 28 | -208864 enst00000411785 sg00000227293 ac118345.1-201 2 66235377 66236213 - lnc_RNA lncrna 29 | 242844 enst00000423168 sg00000232046 linc01798-202 2 66689868 66695581 + lnc_RNA lncrna 30 | 244392 enst00000435389 sg00000232046 linc01798-205 2 66691416 66696804 + lnc_RNA lncrna 31 | 244414 enst00000428590 sg00000232046 linc01798-203 2 66691438 66715630 + lnc_RNA lncrna 32 | 244416 enst00000653254 sg00000232046 linc01798-206 2 66691440 66731223 + lnc_RNA lncrna 33 | 244422 enst00000412944 sg00000232046 linc01798-201 2 66691446 66730157 + lnc_RNA lncrna 34 | 256164 enst00000670163 sg00000237179 linc01797-205 2 66699753 66703188 - lnc_RNA lncrna 35 | 256173 enst00000432410 sg00000237179 linc01797-201 2 66697158 66703197 - lnc_RNA lncrna 36 | 256194 enst00000451698 sg00000237179 linc01797-203 2 66696493 66703218 - lnc_RNA lncrna 37 | 256203 enst00000433432 sg00000237179 linc01797-202 2 66697125 66703227 - lnc_RNA lncrna 38 | 256228 enst00000660433 sg00000237179 linc01797-204 2 66696190 66703252 - lnc_RNA lncrna 39 | -312542 enst00000668467 sg00000204929 ac007389.1-211 2 66132535 66135944 + lnc_RNA lncrna 40 | -359977 enst00000666114 sg00000204929 ac007389.1-210 2 66085100 66200373 + lnc_RNA lncrna 41 | -366619 enst00000607539 sg00000204929 ac007389.1-208 2 66078458 66084638 + lnc_RNA lncrna 42 | -368721 enst00000652861 sg00000204929 ac007389.1-212 2 66076356 66133944 + lnc_RNA lncrna 43 | 375546 enst00000455096 sg00000224071 ac009474.1-201 2 66820684 66822570 - pseudogenic_transcript processed_pseudogene 44 | 434198 enst00000451383 sg00000230355 ac009474.2-201 2 66881087 66881222 - pseudogenic_transcript processed_pseudogene 45 | 457412 enst00000426260 sg00000230525 linc01799-202 2 66904436 66971462 + lnc_RNA lncrna 46 | 458538 enst00000659816 sg00000230525 linc01799-204 2 66905562 66971462 + lnc_RNA lncrna 47 | 458558 enst00000657974 sg00000230525 linc01799-203 2 66905582 66971462 + lnc_RNA lncrna 48 | 473270 enst00000664251 sg00000230525 linc01799-205 2 66920294 66947248 + lnc_RNA lncrna 49 | 474670 enst00000411701 sg00000230525 linc01799-201 2 66921694 66958920 + lnc_RNA lncrna 50 | 475458 enst00000444266 sg00000232688 linc01628-201 2 66921510 66922482 - lnc_RNA lncrna 51 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0024_chr4-80201275-80203807.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -3772 enst00000415738 sg00000152784 prdm8-202 4 80197503 80204329 + mRNA protein_coding 3 | -3865 enst00000653209 sg00000248719 ac021127.1-201 4 80182637 80197410 - lnc_RNA lncrna 4 | -11106 enst00000503589 sg00000248719 ac021127.1-202 4 80183280 80190169 - lnc_RNA lncrna 5 | -15907 enst00000507025 sg00000152784 prdm8-205 4 80185368 80196497 + lnc_RNA processed_transcript 6 | -16005 enst00000339711 sg00000152784 prdm8-201 4 80185270 80204326 + mRNA protein_coding 7 | -16005 enst00000515013 sg00000152784 prdm8-210 4 80185270 80202745 + mRNA protein_coding 8 | -16973 enst00000508061 sg00000152784 prdm8-206 4 80184302 80196601 + lnc_RNA processed_transcript 9 | -16990 enst00000511825 sg00000152784 prdm8-209 4 80184285 80197195 + lnc_RNA processed_transcript 10 | -16990 enst00000504452 sg00000152784 prdm8-203 4 80184285 80204329 + mRNA protein_coding 11 | -17011 enst00000506547 sg00000152784 prdm8-204 4 80184264 80196419 + lnc_RNA processed_transcript 12 | -17394 enst00000509375 sg00000152784 prdm8-208 4 80183881 80197121 + lnc_RNA processed_transcript 13 | -17396 enst00000508965 sg00000152784 prdm8-207 4 80183879 80196598 + lnc_RNA processed_transcript 14 | -40146 enst00000467439 sg00000244002 rpsap39-201 4 80161129 80162011 + pseudogenic_transcript processed_pseudogene 15 | 62792 enst00000312465 sg00000138675 fgf5-201 4 80266599 80290194 + mRNA protein_coding 16 | 62832 enst00000456523 sg00000138675 fgf5-203 4 80266639 80291017 + mRNA protein_coding 17 | 63018 enst00000380628 sg00000138675 fgf5-202 4 80266825 80268518 + lnc_RNA processed_transcript 18 | 63135 enst00000507780 sg00000138675 fgf5-205 4 80266942 80336680 + mRNA nonsense_mediated_decay 19 | 64458 enst00000503413 sg00000138675 fgf5-204 4 80268265 80288958 + lnc_RNA processed_transcript 20 | -75821 enst00000506286 sg00000163297 antxr2-208 4 80069436 80125454 - lnc_RNA processed_transcript 21 | -121675 enst00000514959 sg00000163297 antxr2-209 4 80054281 80079600 - lnc_RNA processed_transcript 22 | -121743 enst00000458289 sg00000236530 kpna2p1-201 4 80079532 80081122 + pseudogenic_transcript processed_pseudogene 23 | -127803 enst00000404191 sg00000163297 antxr2-204 4 79907353 80073472 - mRNA protein_coding 24 | -128046 enst00000403729 sg00000163297 antxr2-203 4 79901146 80073229 - mRNA protein_coding 25 | -128575 enst00000346652 sg00000163297 antxr2-202 4 79977537 80072700 - mRNA protein_coding 26 | -128712 enst00000307333 sg00000163297 antxr2-201 4 79977579 80072563 - mRNA protein_coding 27 | -129655 enst00000449651 sg00000163297 antxr2-205 4 79905571 80071620 - mRNA nonsense_mediated_decay 28 | 131913 enst00000358105 sg00000197826 cfap299-201 4 80335720 80963756 + mRNA protein_coding 29 | 131935 enst00000514249 sg00000197826 cfap299-208 4 80335742 80649206 + mRNA nonsense_mediated_decay 30 | 131935 enst00000512931 sg00000197826 cfap299-206 4 80335742 80649150 + lnc_RNA processed_transcript 31 | 131936 enst00000502497 sg00000197826 cfap299-202 4 80335743 80790507 + lnc_RNA processed_transcript 32 | 131961 enst00000513920 sg00000197826 cfap299-207 4 80335768 80873074 + mRNA nonsense_mediated_decay 33 | 131962 enst00000508675 sg00000197826 cfap299-205 4 80335769 80963612 + mRNA protein_coding 34 | 131974 enst00000503883 sg00000197826 cfap299-203 4 80335781 80583291 + lnc_RNA processed_transcript 35 | 184909 enst00000506637 sg00000232327 ac105917.1-201 4 80386178 80388716 - pseudogenic_transcript processed_pseudogene 36 | -236178 enst00000491345 sg00000163297 antxr2-207 4 79907170 79965097 - lnc_RNA processed_transcript 37 | -236385 enst00000482406 sg00000163297 antxr2-206 4 79906762 79964890 - lnc_RNA processed_transcript 38 | -358173 enst00000391318 sg00000212620 ac118141.1-201 4 79843102 79843228 + snoRNA snorna 39 | -373740 enst00000514836 sg00000251321 pcat4-202 4 79827535 79877770 + lnc_RNA lncrna 40 | -373804 enst00000504263 sg00000251321 pcat4-201 4 79827471 79863247 + lnc_RNA lncrna 41 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0034_chr6-1392675-1394273.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -2264 enst00000611664 sg00000275859 mir6720-201 6 1390314 1390411 - miRNA mirna 3 | -3099 enst00000645481 sg00000137273 foxf2-201 6 1389576 1395603 + mRNA protein_coding 4 | -7609 enst00000568244 sg00000261730 al034346.1-201 6 1383790 1385066 - lnc_RNA lncrna 5 | -68653 enst00000627866 sg00000281809 linc01394-201 6 1321698 1324022 - lnc_RNA lncrna 6 | -80577 enst00000296839 sg00000164379 foxq1-201 6 1312098 1314758 + mRNA protein_coding 7 | 113049 enst00000466002 sg00000243439 rn7sl352p-201 6 1507322 1507598 + ncRNA misc_rna 8 | 121016 enst00000404600 sg00000218027 al512329.1-201 6 1513698 1515289 - pseudogenic_transcript processed_pseudogene 9 | 134638 enst00000607350 sg00000272279 al512329.2-201 6 1528364 1528911 - lnc_RNA lncrna 10 | 207381 enst00000652712 sg00000280916 foxcut-202 6 1601654 1607354 + lnc_RNA lncrna 11 | 211258 enst00000628509 sg00000280916 foxcut-201 6 1605531 1606079 + lnc_RNA lncrna 12 | 215642 enst00000645831 sg00000054598 foxc1-201 6 1609915 1613897 + mRNA protein_coding 13 | 230467 enst00000476972 sg00000112699 gmds-204 6 1623806 1624740 - lnc_RNA processed_transcript 14 | 231228 enst00000467288 sg00000112699 gmds-203 6 1623806 1625501 - lnc_RNA processed_transcript 15 | 231915 enst00000486793 sg00000112699 gmds-205 6 1623806 1626188 - lnc_RNA processed_transcript 16 | -281308 enst00000660745 sg00000286324 al033381.3-201 6 1111367 1114329 + lnc_RNA lncrna 17 | -291275 enst00000664781 sg00000286785 linc01622-206 6 998278 1101400 - lnc_RNA lncrna 18 | -291276 enst00000661526 sg00000286785 linc01622-203 6 1096465 1101399 - lnc_RNA lncrna 19 | -291285 enst00000668813 sg00000286785 linc01622-207 6 1029297 1101390 - lnc_RNA lncrna 20 | -291289 enst00000662378 sg00000286785 linc01622-204 6 961000 1101386 - lnc_RNA lncrna 21 | -291294 enst00000663447 sg00000286785 linc01622-205 6 1098829 1101381 - lnc_RNA lncrna 22 | -291303 enst00000655659 sg00000286785 linc01622-202 6 958323 1101372 - lnc_RNA lncrna 23 | -292406 enst00000612554 sg00000286785 linc01622-201 6 958338 1100269 - lnc_RNA lncrna 24 | -312746 enst00000314040 sg00000176515 al033381.1-201 6 1079929 1104946 + lnc_RNA lncrna 25 | 332204 enst00000533279 sg00000112699 gmds-210 6 1679172 1726477 - lnc_RNA processed_transcript 26 | -365450 enst00000603854 sg00000270937 al033381.2-201 6 1026494 1027225 - lnc_RNA lncrna 27 | -388955 enst00000669177 sg00000286785 linc01622-208 6 997024 1003720 - lnc_RNA lncrna 28 | -483669 enst00000620188 sg00000276687 al356130.1-201 6 905445 909006 - lnc_RNA lncrna 29 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0057_chr2-154698540-154699822.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000544049 sg00000162989 kcnj3-203 2 154698581 154858352 + mRNA protein_coding 3 | 0 enst00000295101 sg00000162989 kcnj3-201 2 154698695 154858354 + mRNA protein_coding 4 | -685 enst00000651198 sg00000162989 kcnj3-204 2 154697855 154857873 + mRNA protein_coding 5 | -723 enst00000443901 sg00000287900 ac061961.1-201 2 154696462 154697817 - lnc_RNA lncrna 6 | -833 enst00000654516 sg00000287900 ac061961.1-202 2 154688296 154697707 - lnc_RNA lncrna 7 | -3603 enst00000662205 sg00000287900 ac061961.1-203 2 154689392 154694937 - lnc_RNA lncrna 8 | 9510 enst00000493505 sg00000162989 kcnj3-202 2 154709332 154855028 + lnc_RNA processed_transcript 9 | -108133 enst00000411358 sg00000223290 rna5sp107-201 2 154590407 154590528 + pseudogenic_transcript rrna_pseudogene 10 | -238683 enst00000432599 sg00000238004 ac009227.2-201 2 154459857 154460820 + lnc_RNA lncrna 11 | -241102 enst00000434635 sg00000224675 ac009227.1-201 2 154435853 154457438 - lnc_RNA lncrna 12 | 241245 enst00000430257 sg00000228837 cbx3p6-201 2 154940541 154941067 - pseudogenic_transcript processed_pseudogene 13 | -252062 enst00000494805 sg00000144278 galnt13-210 2 154446478 154450694 + lnc_RNA retained_intron 14 | -256819 enst00000489553 sg00000144278 galnt13-209 2 154441721 154450801 + lnc_RNA processed_transcript 15 | -259948 enst00000453715 sg00000144278 galnt13-207 2 154438592 154450745 + mRNA protein_coding 16 | 269279 enst00000442706 sg00000230991 ac092625.1-201 2 154964308 154969101 - lnc_RNA lncrna 17 | -289529 enst00000422126 sg00000144278 galnt13-203 2 154409011 154450793 + mRNA protein_coding 18 | 389716 enst00000411265 sg00000223197 rnu6-1001p-201 2 155089439 155089538 - snRNA snrna 19 | -396961 enst00000450838 sg00000144278 galnt13-206 2 154301579 154450730 + mRNA protein_coding 20 | -411951 enst00000437447 sg00000230251 phbp4-201 2 154286589 154287425 + pseudogenic_transcript processed_pseudogene 21 | -440973 enst00000487047 sg00000144278 galnt13-208 2 154257567 154438676 + lnc_RNA processed_transcript 22 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0066_chr5-3601878-3603265.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -1690 enst00000559410 sg00000259603 ac016595.1-201 5 3596211 3600188 - lnc_RNA lncrna 3 | -6046 enst00000302006 sg00000170549 irx1-201 5 3595832 3601403 + mRNA protein_coding 4 | -65784 enst00000505443 sg00000248118 linc01019-201 5 3417152 3536094 - lnc_RNA lncrna 5 | -70083 enst00000662836 sg00000248118 linc01019-202 5 3357264 3531795 - lnc_RNA lncrna 6 | -97874 enst00000508823 sg00000250716 linc01017-201 5 3496229 3504004 - lnc_RNA lncrna 7 | -149062 enst00000512521 sg00000249830 linc02162-201 5 3452816 3461660 + lnc_RNA lncrna 8 | 410384 enst00000513859 sg00000248962 ac025773.1-201 5 4012708 4013649 - lnc_RNA lncrna 9 | -424015 enst00000652864 sg00000249808 ac091832.1-202 5 3177863 3181487 + lnc_RNA lncrna 10 | -424043 enst00000505396 sg00000249808 ac091832.1-201 5 3177835 3181232 + lnc_RNA lncrna 11 | 438499 enst00000506305 sg00000249994 ac025187.1-201 5 4033713 4041764 - lnc_RNA lncrna 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0072_chr16-54288263-54289879.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 1086 enst00000616682 sg00000277559 ac018553.1-201 16 54290965 54292422 + lnc_RNA lncrna 3 | -1476 enst00000329734 sg00000177508 irx3-201 16 54283304 54286787 - mRNA protein_coding 4 | -1539 enst00000558180 sg00000177508 irx3-203 16 54284120 54286724 - lnc_RNA retained_intron 5 | -2408 enst00000558054 sg00000177508 irx3-202 16 54283436 54285855 - mRNA protein_coding 6 | -2659 enst00000637770 sg00000283689 ac018553.2-201 16 54285604 54289568 + lnc_RNA lncrna 7 | -17384 enst00000649252 sg00000259517 linc02169-202 16 54245544 54270879 - lnc_RNA lncrna 8 | -17517 enst00000561336 sg00000259517 linc02169-201 16 54245618 54270746 - lnc_RNA lncrna 9 | -48570 enst00000557953 sg00000259759 ac007907.1-201 16 54239693 54240654 + lnc_RNA lncrna 10 | 80385 enst00000660155 sg00000261803 linc02140-203 16 54365996 54370264 - lnc_RNA lncrna 11 | 80386 enst00000663832 sg00000287885 ac018553.3-201 16 54370265 54374728 + lnc_RNA lncrna 12 | 80562 enst00000668085 sg00000261803 linc02140-205 16 54365996 54370441 - lnc_RNA lncrna 13 | 80581 enst00000669832 sg00000261803 linc02140-206 16 54366001 54370460 - lnc_RNA lncrna 14 | 80786 enst00000566649 sg00000261803 linc02140-202 16 54366007 54370665 - lnc_RNA lncrna 15 | 80820 enst00000562614 sg00000261803 linc02140-201 16 54367367 54370699 - lnc_RNA lncrna 16 | 80915 enst00000661222 sg00000261803 linc02140-204 16 54365996 54370794 - lnc_RNA lncrna 17 | -138573 enst00000637049 sg00000140718 fto-218 16 54149690 54158512 + mRNA nonsense_mediated_decay 18 | -173385 enst00000623044 sg00000280454 ac007347.2-201 16 54114697 54114878 - pseudogenic_transcript pseudogene 19 | 201517 enst00000660981 sg00000286845 ac007343.1-201 16 54490281 54491396 - lnc_RNA lncrna 20 | -218367 enst00000636091 sg00000140718 fto-213 16 54069896 54114439 + lnc_RNA processed_transcript 21 | -224626 enst00000472835 sg00000140718 fto-207 16 54063637 54112302 + lnc_RNA processed_transcript 22 | -233680 enst00000563879 sg00000261049 ac007347.1-201 16 54033997 54054583 - lnc_RNA lncrna 23 | 269221 enst00000637822 sg00000283304 linc02183-201 16 54542808 54559100 - lnc_RNA lncrna 24 | -288294 enst00000565641 sg00000260194 ac007496.1-201 16 53998313 53999969 - lnc_RNA lncrna 25 | -297251 enst00000624987 sg00000280392 ac007496.3-201 16 53991012 53994454 + unconfirmed_transcript tec 26 | -306351 enst00000564801 sg00000261630 ac007496.2-201 16 53981229 53981912 - lnc_RNA lncrna 27 | 344458 enst00000637961 sg00000283258 ac007491.1-202 16 54631754 54634337 - lnc_RNA lncrna 28 | -354233 enst00000268349 sg00000140718 fto-201 16 53934030 54114463 + mRNA protein_coding 29 | -365207 enst00000635892 sg00000140718 fto-211 16 53923056 54112632 + lnc_RNA processed_transcript 30 | 367783 enst00000637560 sg00000283258 ac007491.1-201 16 54628963 54657662 - lnc_RNA lncrna 31 | -377007 enst00000463855 sg00000140718 fto-204 16 53911256 54114463 + mRNA protein_coding 32 | -399369 enst00000637062 sg00000140718 fto-219 16 53888894 53935847 + mRNA protein_coding 33 | -401333 enst00000460382 sg00000140718 fto-203 16 53886930 54112987 + mRNA protein_coding 34 | -401346 enst00000431610 sg00000140718 fto-202 16 53886917 54112138 + mRNA protein_coding 35 | -408419 enst00000612285 sg00000140718 fto-210 16 53879844 54153448 + mRNA protein_coding 36 | -461902 enst00000563011 sg00000140718 fto-208 16 53826361 54040726 + mRNA protein_coding 37 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0073_chr5-3599098-3600332.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000559410 sg00000259603 ac016595.1-201 5 3596211 3600188 - lnc_RNA lncrna 3 | -3266 enst00000302006 sg00000170549 irx1-201 5 3595832 3601403 + mRNA protein_coding 4 | -63004 enst00000505443 sg00000248118 linc01019-201 5 3417152 3536094 - lnc_RNA lncrna 5 | -67303 enst00000662836 sg00000248118 linc01019-202 5 3357264 3531795 - lnc_RNA lncrna 6 | -95094 enst00000508823 sg00000250716 linc01017-201 5 3496229 3504004 - lnc_RNA lncrna 7 | -146282 enst00000512521 sg00000249830 linc02162-201 5 3452816 3461660 + lnc_RNA lncrna 8 | 413317 enst00000513859 sg00000248962 ac025773.1-201 5 4012708 4013649 - lnc_RNA lncrna 9 | -421235 enst00000652864 sg00000249808 ac091832.1-202 5 3177863 3181487 + lnc_RNA lncrna 10 | -421263 enst00000505396 sg00000249808 ac091832.1-201 5 3177835 3181232 + lnc_RNA lncrna 11 | 441432 enst00000506305 sg00000249994 ac025187.1-201 5 4033713 4041764 - lnc_RNA lncrna 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0075_chr10-93059948-93061756.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000624358 sg00000187553 cyp26c1-201 10 93060808 93069536 + mRNA nonsense_mediated_decay 3 | 0 enst00000651965 sg00000187553 cyp26c1-202 10 93060798 93069540 + mRNA protein_coding 4 | 0 enst00000444965 sg00000226425 al358613.1-201 10 93059663 93060426 - lnc_RNA lncrna 5 | 1890 enst00000648258 sg00000285846 al358613.3-201 10 93063646 93077424 + lnc_RNA lncrna 6 | 10216 enst00000624651 sg00000279607 al358613.2-201 10 93071972 93073466 + lnc_RNA lncrna 7 | 11719 enst00000371531 sg00000095596 cyp26a1-202 10 93073475 93077884 + mRNA protein_coding 8 | 12137 enst00000224356 sg00000095596 cyp26a1-201 10 93073893 93077885 + mRNA protein_coding 9 | 12322 enst00000622925 sg00000095596 cyp26a1-203 10 93074078 93075275 + lnc_RNA retained_intron 10 | 12556 enst00000624589 sg00000095596 cyp26a1-205 10 93074312 93077479 + mRNA nonsense_mediated_decay 11 | 13873 enst00000623162 sg00000095596 cyp26a1-204 10 93075629 93077319 + lnc_RNA retained_intron 12 | 14577 enst00000625202 sg00000095596 cyp26a1-206 10 93076333 93077082 + lnc_RNA retained_intron 13 | 45627 enst00000433227 sg00000232805 nip7p1-201 10 93106872 93107383 - pseudogenic_transcript processed_pseudogene 14 | -62474 enst00000458552 sg00000138190 exoc6-205 10 92997474 93014267 + mRNA protein_coding 15 | -131574 enst00000495132 sg00000138190 exoc6-206 10 92928374 93058524 + mRNA nonsense_mediated_decay 16 | 147871 enst00000420392 sg00000237417 xrcc6p1-201 10 93206857 93209627 - pseudogenic_transcript processed_pseudogene 17 | -150464 enst00000497262 sg00000138190 exoc6-207 10 92909484 92916030 + lnc_RNA processed_transcript 18 | -181659 enst00000447000 sg00000225118 al392103.1-201 10 92878092 92878289 - pseudogenic_transcript processed_pseudogene 19 | -211428 enst00000260762 sg00000138190 exoc6-201 10 92848520 93059490 + mRNA protein_coding 20 | -211463 enst00000371543 sg00000138190 exoc6-202 10 92848485 92901851 + mRNA protein_coding 21 | -211480 enst00000443748 sg00000138190 exoc6-204 10 92848468 93059493 + mRNA protein_coding 22 | 222802 enst00000394133 sg00000213432 rpl17p34-201 10 93284004 93284558 - pseudogenic_transcript processed_pseudogene 23 | -225235 enst00000371552 sg00000138190 exoc6-203 10 92834713 93059493 + mRNA protein_coding 24 | -228770 enst00000672817 sg00000138190 exoc6-209 10 92831178 93058590 + mRNA protein_coding 25 | -233117 enst00000671701 sg00000138190 exoc6-208 10 92826831 93059493 + mRNA protein_coding 26 | 261919 enst00000474161 sg00000138119 myof-206 10 93323118 93323675 - lnc_RNA retained_intron 27 | 268017 enst00000485212 sg00000138119 myof-208 10 93324270 93329773 - lnc_RNA processed_transcript 28 | 278493 enst00000475358 sg00000138119 myof-207 10 93337528 93340249 - lnc_RNA processed_transcript 29 | 318231 enst00000463743 sg00000138119 myof-205 10 93306429 93379987 - mRNA nonsense_mediated_decay 30 | -349340 enst00000364542 sg00000201412 al590080.1-201 10 92710499 92710608 - ncRNA misc_rna 31 | -367916 enst00000492654 sg00000152804 hhex-203 10 92692032 92694788 + mRNA protein_coding 32 | -368128 enst00000472590 sg00000152804 hhex-202 10 92691820 92695641 + mRNA protein_coding 33 | -369993 enst00000551454 sg00000152804 hhex-204 10 92689955 92692483 + lnc_RNA retained_intron 34 | -369993 enst00000282728 sg00000152804 hhex-201 10 92689955 92695647 + mRNA protein_coding 35 | -390205 enst00000428356 sg00000236493 eif2s2p3-201 10 92668745 92669743 - pseudogenic_transcript processed_pseudogene 36 | -400904 enst00000577919 sg00000264313 rn7sl644p-201 10 92659044 92659302 + ncRNA misc_rna 37 | 420438 enst00000371488 sg00000138119 myof-203 10 93425741 93482194 - mRNA protein_coding 38 | 420438 enst00000358334 sg00000138119 myof-201 10 93306430 93482194 - mRNA protein_coding 39 | 420438 enst00000488645 sg00000138119 myof-209 10 93426071 93482194 - lnc_RNA processed_transcript 40 | 420561 enst00000371489 sg00000138119 myof-204 10 93397185 93482317 - mRNA protein_coding 41 | 420578 enst00000359263 sg00000138119 myof-202 10 93306429 93482334 - mRNA protein_coding 42 | 434856 enst00000371485 sg00000138180 cep55-201 10 93496612 93529092 + mRNA protein_coding 43 | 445254 enst00000445435 sg00000138180 cep55-202 10 93507010 93519111 + mRNA protein_coding 44 | 448924 enst00000391094 sg00000212396 rna5sp323-201 10 93510548 93510680 - pseudogenic_transcript rrna_pseudogene 45 | 455451 enst00000496302 sg00000138180 cep55-203 10 93517207 93520277 + lnc_RNA processed_transcript 46 | -462661 enst00000332269 sg00000184111 rpl11p4-201 10 92596852 92597287 - pseudogenic_transcript processed_pseudogene 47 | -466818 enst00000260731 sg00000138160 kif11-201 10 92593130 92655395 + mRNA protein_coding 48 | -485855 enst00000265986 sg00000119912 ide-201 10 92451684 92574093 - mRNA protein_coding 49 | -485872 enst00000650060 sg00000119912 ide-209 10 92451684 92574076 - mRNA protein_coding 50 | -485881 enst00000478361 sg00000119912 ide-206 10 92474472 92574067 - mRNA nonsense_mediated_decay 51 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0080_chr10-86363012-86364273.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2220 enst00000464741 sg00000182771 grid1-202 10 85601994 86366493 - mRNA nonsense_mediated_decay 3 | 2522 enst00000327946 sg00000182771 grid1-201 10 85599552 86366795 - mRNA protein_coding 4 | 35862 enst00000656749 sg00000287475 al844892.2-202 10 86395195 86400135 - lnc_RNA lncrna 5 | 36060 enst00000660918 sg00000287475 al844892.2-203 10 86395457 86400333 - lnc_RNA lncrna 6 | 36670 enst00000670831 sg00000287475 al844892.2-201 10 86395187 86400943 - lnc_RNA lncrna 7 | 38928 enst00000671245 sg00000286359 al844892.1-201 10 86402119 86403201 - lnc_RNA lncrna 8 | 79759 enst00000484070 sg00000062650 wapl-204 10 86435256 86444032 - lnc_RNA retained_intron 9 | -98224 enst00000362234 sg00000199104 mir346-201 10 86264694 86264788 - miRNA mirna 10 | 103233 enst00000372075 sg00000062650 wapl-203 10 86437010 86467506 - mRNA protein_coding 11 | 108014 enst00000489996 sg00000062650 wapl-205 10 86467053 86472287 - lnc_RNA processed_transcript 12 | 124173 enst00000391030 sg00000212332 rnu6-780p-201 10 86488446 86488549 + snRNA snrna 13 | 157495 enst00000263070 sg00000062650 wapl-201 10 86435257 86521768 - mRNA protein_coding 14 | 157495 enst00000618527 sg00000062650 wapl-206 10 86435257 86521768 - mRNA protein_coding 15 | 157519 enst00000298767 sg00000062650 wapl-202 10 86435256 86521792 - mRNA protein_coding 16 | 157672 enst00000428940 sg00000227896 al731569.1-201 10 86521945 86525101 + lnc_RNA lncrna 17 | 267355 enst00000481963 sg00000230507 rpl7ap8-201 10 86630825 86631628 - pseudogenic_transcript processed_pseudogene 18 | 290274 enst00000241891 sg00000122375 opn4-201 10 86654547 86666460 + mRNA protein_coding 19 | 290284 enst00000372071 sg00000122375 opn4-202 10 86654557 86666455 + mRNA protein_coding 20 | 290344 enst00000443292 sg00000122375 opn4-203 10 86654617 86666848 + mRNA protein_coding 21 | 304176 enst00000429277 sg00000122367 ldb3-205 10 86668449 86736068 + mRNA protein_coding 22 | 304234 enst00000623056 sg00000122367 ldb3-209 10 86668507 86733001 + mRNA protein_coding 23 | 304340 enst00000372066 sg00000122367 ldb3-204 10 86668613 86700041 + mRNA protein_coding 24 | 304398 enst00000361373 sg00000122367 ldb3-202 10 86668671 86736068 + mRNA protein_coding 25 | 304419 enst00000623007 sg00000122367 ldb3-208 10 86668692 86700045 + mRNA protein_coding 26 | 304419 enst00000263066 sg00000122367 ldb3-201 10 86668692 86734995 + mRNA protein_coding 27 | 304419 enst00000372056 sg00000122367 ldb3-203 10 86668692 86700045 + mRNA protein_coding 28 | 304419 enst00000542786 sg00000122367 ldb3-207 10 86668692 86700043 + mRNA protein_coding 29 | -310564 enst00000363617 sg00000200487 rna5sp322-201 10 86052448 86052566 + pseudogenic_transcript rrna_pseudogene 30 | 354457 enst00000477489 sg00000122367 ldb3-206 10 86718730 86726451 + mRNA protein_coding 31 | 392025 enst00000608826 sg00000272631 ac067750.1-201 10 86749754 86756298 - lnc_RNA lncrna 32 | 392328 enst00000638429 sg00000107779 bmpr1a-205 10 86756601 86932825 + mRNA nonsense_mediated_decay 33 | 392377 enst00000372037 sg00000107779 bmpr1a-201 10 86756650 86932838 + mRNA protein_coding 34 | 474589 enst00000636056 sg00000107779 bmpr1a-204 10 86838862 86929738 + mRNA nonsense_mediated_decay 35 | 474589 enst00000635816 sg00000107779 bmpr1a-203 10 86838862 86929746 + mRNA nonsense_mediated_decay 36 | 474666 enst00000480152 sg00000107779 bmpr1a-202 10 86838939 86890117 + mRNA protein_coding 37 | 491963 enst00000603626 sg00000270874 rpap2p1-201 10 86854696 86856236 - pseudogenic_transcript processed_pseudogene 38 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0089_chr16-54281497-54282666.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2938 enst00000637770 sg00000283689 ac018553.2-201 16 54285604 54289568 + lnc_RNA lncrna 3 | 3189 enst00000558054 sg00000177508 irx3-202 16 54283436 54285855 - mRNA protein_coding 4 | 4058 enst00000558180 sg00000177508 irx3-203 16 54284120 54286724 - lnc_RNA retained_intron 5 | 4121 enst00000329734 sg00000177508 irx3-201 16 54283304 54286787 - mRNA protein_coding 6 | 8299 enst00000616682 sg00000277559 ac018553.1-201 16 54290965 54292422 + lnc_RNA lncrna 7 | -10618 enst00000649252 sg00000259517 linc02169-202 16 54245544 54270879 - lnc_RNA lncrna 8 | -10751 enst00000561336 sg00000259517 linc02169-201 16 54245618 54270746 - lnc_RNA lncrna 9 | -41804 enst00000557953 sg00000259759 ac007907.1-201 16 54239693 54240654 + lnc_RNA lncrna 10 | 87598 enst00000660155 sg00000261803 linc02140-203 16 54365996 54370264 - lnc_RNA lncrna 11 | 87599 enst00000663832 sg00000287885 ac018553.3-201 16 54370265 54374728 + lnc_RNA lncrna 12 | 87775 enst00000668085 sg00000261803 linc02140-205 16 54365996 54370441 - lnc_RNA lncrna 13 | 87794 enst00000669832 sg00000261803 linc02140-206 16 54366001 54370460 - lnc_RNA lncrna 14 | 87999 enst00000566649 sg00000261803 linc02140-202 16 54366007 54370665 - lnc_RNA lncrna 15 | 88033 enst00000562614 sg00000261803 linc02140-201 16 54367367 54370699 - lnc_RNA lncrna 16 | 88128 enst00000661222 sg00000261803 linc02140-204 16 54365996 54370794 - lnc_RNA lncrna 17 | -131807 enst00000637049 sg00000140718 fto-218 16 54149690 54158512 + mRNA nonsense_mediated_decay 18 | -166619 enst00000623044 sg00000280454 ac007347.2-201 16 54114697 54114878 - pseudogenic_transcript pseudogene 19 | 208730 enst00000660981 sg00000286845 ac007343.1-201 16 54490281 54491396 - lnc_RNA lncrna 20 | -211601 enst00000636091 sg00000140718 fto-213 16 54069896 54114439 + lnc_RNA processed_transcript 21 | -217860 enst00000472835 sg00000140718 fto-207 16 54063637 54112302 + lnc_RNA processed_transcript 22 | -226914 enst00000563879 sg00000261049 ac007347.1-201 16 54033997 54054583 - lnc_RNA lncrna 23 | 276434 enst00000637822 sg00000283304 linc02183-201 16 54542808 54559100 - lnc_RNA lncrna 24 | -281528 enst00000565641 sg00000260194 ac007496.1-201 16 53998313 53999969 - lnc_RNA lncrna 25 | -290485 enst00000624987 sg00000280392 ac007496.3-201 16 53991012 53994454 + unconfirmed_transcript tec 26 | -299585 enst00000564801 sg00000261630 ac007496.2-201 16 53981229 53981912 - lnc_RNA lncrna 27 | -347467 enst00000268349 sg00000140718 fto-201 16 53934030 54114463 + mRNA protein_coding 28 | 351671 enst00000637961 sg00000283258 ac007491.1-202 16 54631754 54634337 - lnc_RNA lncrna 29 | -358441 enst00000635892 sg00000140718 fto-211 16 53923056 54112632 + lnc_RNA processed_transcript 30 | -370241 enst00000463855 sg00000140718 fto-204 16 53911256 54114463 + mRNA protein_coding 31 | 374996 enst00000637560 sg00000283258 ac007491.1-201 16 54628963 54657662 - lnc_RNA lncrna 32 | -392603 enst00000637062 sg00000140718 fto-219 16 53888894 53935847 + mRNA protein_coding 33 | -394567 enst00000460382 sg00000140718 fto-203 16 53886930 54112987 + mRNA protein_coding 34 | -394580 enst00000431610 sg00000140718 fto-202 16 53886917 54112138 + mRNA protein_coding 35 | -401653 enst00000612285 sg00000140718 fto-210 16 53879844 54153448 + mRNA protein_coding 36 | -455136 enst00000563011 sg00000140718 fto-208 16 53826361 54040726 + mRNA protein_coding 37 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0090_chr8-140099765-140101001.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000631594 sg00000282164 peg13-201 8 140094894 140100543 - lnc_RNA lncrna 3 | -17612 enst00000523777 sg00000167632 trappc9-214 8 139732162 140082153 - lnc_RNA processed_transcript 4 | -60009 enst00000617244 sg00000274064 ac040978.1-201 8 140039756 140041037 + pseudogenic_transcript processed_pseudogene 5 | -91174 enst00000524162 sg00000167632 trappc9-215 8 139732093 140008591 - lnc_RNA processed_transcript 6 | 137492 enst00000517667 sg00000167632 trappc9-203 8 139988740 140238493 - lnc_RNA processed_transcript 7 | 161729 enst00000518839 sg00000167632 trappc9-205 8 140215910 140262730 - lnc_RNA processed_transcript 8 | 161730 enst00000520532 sg00000167632 trappc9-207 8 139988823 140262731 - lnc_RNA processed_transcript 9 | -168593 enst00000507535 sg00000250733 c8orf17-201 8 139931172 139933942 + unconfirmed_transcript tec 10 | -168593 enst00000625034 sg00000250733 c8orf17-202 8 139931172 139933946 + unconfirmed_transcript tec 11 | 174752 enst00000634178 sg00000167632 trappc9-216 8 140252571 140275753 - mRNA protein_coding 12 | -184966 enst00000521883 sg00000253574 ac021744.1-202 8 139914799 139916620 + lnc_RNA lncrna 13 | -188527 enst00000518354 sg00000253574 ac021744.1-201 8 139911238 139916620 + lnc_RNA lncrna 14 | 190250 enst00000521667 sg00000167632 trappc9-210 8 139730892 140291251 - lnc_RNA retained_intron 15 | -191007 enst00000519482 sg00000167632 trappc9-206 8 139731044 139908758 - lnc_RNA processed_transcript 16 | -191070 enst00000518723 sg00000167632 trappc9-204 8 139904432 139908695 - lnc_RNA retained_intron 17 | 201834 enst00000521167 sg00000167632 trappc9-209 8 140283987 140302835 - lnc_RNA processed_transcript 18 | -218470 enst00000522504 sg00000167632 trappc9-213 8 139730996 139881295 - lnc_RNA processed_transcript 19 | -293532 enst00000521700 sg00000167632 trappc9-211 8 139731006 139806233 - lnc_RNA processed_transcript 20 | 334196 enst00000521944 sg00000167632 trappc9-212 8 140405293 140435197 - lnc_RNA retained_intron 21 | 349929 enst00000520857 sg00000167632 trappc9-208 8 139730345 140450930 - mRNA protein_coding 22 | 356743 enst00000438773 sg00000167632 trappc9-202 8 139730343 140457744 - mRNA protein_coding 23 | 357578 enst00000389328 sg00000167632 trappc9-201 8 139730343 140458579 - mRNA protein_coding 24 | 357578 enst00000648948 sg00000167632 trappc9-217 8 139727725 140458579 - mRNA protein_coding 25 | -395656 enst00000648164 sg00000169427 kcnk9-208 8 139617121 139704109 - mRNA protein_coding 26 | -396642 enst00000520439 sg00000169427 kcnk9-203 8 139617121 139703123 - mRNA protein_coding 27 | -396672 enst00000650269 sg00000169427 kcnk9-212 8 139601097 139703093 - mRNA protein_coding 28 | -396724 enst00000522317 sg00000169427 kcnk9-204 8 139600838 139703041 - mRNA nonsense_mediated_decay 29 | -396767 enst00000303015 sg00000169427 kcnk9-201 8 139612561 139702998 - mRNA protein_coding 30 | -396809 enst00000649473 sg00000169427 kcnk9-210 8 139600839 139702956 - mRNA nonsense_mediated_decay 31 | 407042 enst00000564464 sg00000259891 ac107375.1-201 8 140505813 140508043 - lnc_RNA lncrna 32 | 410310 enst00000519533 sg00000104472 chrac1-203 8 140511311 140516467 + mRNA protein_coding 33 | 410321 enst00000220913 sg00000104472 chrac1-201 8 140511322 140517154 + mRNA protein_coding 34 | 410917 enst00000518971 sg00000104472 chrac1-202 8 140511918 140515185 + mRNA protein_coding 35 | 410981 enst00000519618 sg00000104472 chrac1-204 8 140511982 140515765 + mRNA protein_coding 36 | 413293 enst00000523569 sg00000104472 chrac1-205 8 140514294 140515541 + lnc_RNA retained_intron 37 | 431705 enst00000520628 sg00000123908 ago2-207 8 140532094 140532706 - lnc_RNA processed_transcript 38 | 438448 enst00000519347 sg00000123908 ago2-204 8 140535391 140539449 - lnc_RNA retained_intron 39 | 440456 enst00000520412 sg00000123908 ago2-206 8 140532533 140541457 - lnc_RNA retained_intron 40 | -445415 enst00000523477 sg00000169427 kcnk9-205 8 139600845 139654350 - lnc_RNA processed_transcript 41 | -445435 enst00000647605 sg00000169427 kcnk9-207 8 139617159 139654330 - mRNA protein_coding 42 | -445435 enst00000649696 sg00000169427 kcnk9-211 8 139600845 139654330 - mRNA nonsense_mediated_decay 43 | 455237 enst00000521325 sg00000123908 ago2-208 8 140555408 140556238 - lnc_RNA retained_intron 44 | -465904 enst00000648481 sg00000169427 kcnk9-209 8 139617206 139633861 - lnc_RNA processed_transcript 45 | 471811 enst00000624190 sg00000279766 ac067931.1-201 8 140572142 140572812 - unconfirmed_transcript tec 46 | -483718 enst00000519923 sg00000169427 kcnk9-202 8 139612326 139616047 - lnc_RNA processed_transcript 47 | 490683 enst00000624905 sg00000280326 ac067931.2-201 8 140591684 140593201 + unconfirmed_transcript tec 48 | -497701 enst00000523653 sg00000169427 kcnk9-206 8 139601078 139602064 - lnc_RNA processed_transcript 49 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0099_chr8-9898069-9899160.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2040 enst00000518557 sg00000253230 linc00599-202 8 9900064 9901200 - lnc_RNA lncrna 3 | 2653 enst00000662006 sg00000253230 linc00599-210 8 9900064 9901813 - lnc_RNA lncrna 4 | 2777 enst00000666267 sg00000253230 linc00599-212 8 9900058 9901937 - lnc_RNA lncrna 5 | 4237 enst00000517675 sg00000253230 linc00599-201 8 9900064 9903397 - lnc_RNA lncrna 6 | 4238 enst00000669913 sg00000253230 linc00599-215 8 9900077 9903398 - lnc_RNA lncrna 7 | 4238 enst00000654192 sg00000253230 linc00599-207 8 9900071 9903398 - lnc_RNA lncrna 8 | 4238 enst00000665174 sg00000253230 linc00599-211 8 9900064 9903398 - lnc_RNA lncrna 9 | 4238 enst00000653424 sg00000253230 linc00599-206 8 9900064 9903398 - lnc_RNA lncrna 10 | 4238 enst00000519461 sg00000253230 linc00599-203 8 9900064 9903398 - lnc_RNA lncrna 11 | 4238 enst00000667273 sg00000253230 linc00599-214 8 9899871 9903398 - lnc_RNA lncrna 12 | 4238 enst00000667251 sg00000253230 linc00599-213 8 9899944 9903398 - lnc_RNA lncrna 13 | 4312 enst00000385275 sg00000284321 mir124-1-201 8 9903388 9903472 - miRNA mirna 14 | 5050 enst00000521863 sg00000253230 linc00599-205 8 9903167 9904210 - lnc_RNA lncrna 15 | 6098 enst00000656078 sg00000253230 linc00599-208 8 9900064 9905258 - lnc_RNA lncrna 16 | 6206 enst00000521242 sg00000253230 linc00599-204 8 9903461 9905366 - lnc_RNA lncrna 17 | 7518 enst00000661494 sg00000253230 linc00599-209 8 9904893 9906678 - lnc_RNA lncrna 18 | -127938 enst00000517770 sg00000173273 tnks-203 8 9770131 9777036 + mRNA protein_coding 19 | 155094 enst00000562143 sg00000260093 ac034111.1-201 8 10050485 10054254 - lnc_RNA lncrna 20 | 155132 enst00000317173 sg00000175806 msra-201 8 10054292 10428891 + mRNA protein_coding 21 | 155210 enst00000441698 sg00000175806 msra-203 8 10054370 10428365 + mRNA protein_coding 22 | 155341 enst00000518255 sg00000175806 msra-205 8 10054501 10337823 + mRNA protein_coding 23 | 155881 enst00000659604 sg00000286622 ac034111.2-201 8 9984004 10055041 - lnc_RNA lncrna 24 | -156397 enst00000384968 sg00000207701 mir597-201 8 9741672 9741768 + miRNA mirna 25 | -157155 enst00000519191 sg00000173273 tnks-208 8 9740914 9751713 + lnc_RNA processed_transcript 26 | 159810 enst00000521209 sg00000175806 msra-206 8 10058970 10250917 + mRNA protein_coding 27 | -163078 enst00000518635 sg00000173273 tnks-207 8 9734991 9748213 + mRNA nonsense_mediated_decay 28 | -177613 enst00000519930 sg00000173273 tnks-210 8 9720456 9730973 + lnc_RNA processed_transcript 29 | 196391 enst00000522907 sg00000175806 msra-208 8 10095551 10319891 + mRNA protein_coding 30 | 196392 enst00000528246 sg00000175806 msra-210 8 10095552 10428885 + mRNA protein_coding 31 | 196567 enst00000382490 sg00000175806 msra-202 8 10095727 10428889 + mRNA protein_coding 32 | 196567 enst00000523637 sg00000175806 msra-209 8 10095727 10320363 + lnc_RNA retained_intron 33 | -218223 enst00000517989 sg00000173273 tnks-204 8 9679846 9708406 + lnc_RNA retained_intron 34 | -218315 enst00000519392 sg00000173273 tnks-209 8 9679754 9707008 + lnc_RNA processed_transcript 35 | -227950 enst00000521039 sg00000173273 tnks-212 8 9670119 9681156 + lnc_RNA retained_intron 36 | -239631 enst00000520383 sg00000253697 ac103834.1-201 8 9658295 9658438 - pseudogenic_transcript unprocessed_pseudogene 37 | 248263 enst00000649481 sg00000285675 ac023385.1-201 8 10118005 10147423 - lnc_RNA lncrna 38 | -282779 enst00000518027 sg00000173273 tnks-205 8 9615290 9707008 + lnc_RNA processed_transcript 39 | -323062 enst00000518281 sg00000173273 tnks-206 8 9575007 9776929 + mRNA protein_coding 40 | -331809 enst00000517652 sg00000173273 tnks-202 8 9566260 9566526 + lnc_RNA processed_transcript 41 | -341549 enst00000607598 sg00000272267 ac021242.3-201 8 9555144 9556520 - lnc_RNA lncrna 42 | -342137 enst00000522110 sg00000173273 tnks-213 8 9555932 9558831 + mRNA protein_coding 43 | -342155 enst00000520408 sg00000173273 tnks-211 8 9555914 9710409 + mRNA protein_coding 44 | -342157 enst00000310430 sg00000173273 tnks-201 8 9555912 9782346 + mRNA protein_coding 45 | 380577 enst00000648351 sg00000285606 ac079200.1-201 8 10275499 10279737 - lnc_RNA lncrna 46 | 402375 enst00000521686 sg00000175806 msra-207 8 10301535 10353963 + mRNA protein_coding 47 | 427308 enst00000517594 sg00000175806 msra-204 8 10326468 10411565 + lnc_RNA processed_transcript 48 | 438517 enst00000513168 sg00000249848 ac112673.1-201 8 10336782 10337677 - pseudogenic_transcript processed_pseudogene 49 | -444371 enst00000507315 sg00000249050 ac021242.1-201 8 9453698 9457418 + pseudogenic_transcript processed_pseudogene 50 | -461864 enst00000522129 sg00000254237 ac021242.2-202 8 9374898 9436205 - lnc_RNA lncrna 51 | -482086 enst00000521842 sg00000254237 ac021242.2-203 8 9379975 9415983 - lnc_RNA lncrna 52 | -493763 enst00000647946 sg00000248538 ac022784.1-268 8 9404306 9413869 + lnc_RNA lncrna 53 | -495107 enst00000649974 sg00000248538 ac022784.1-267 8 9402962 9413878 + lnc_RNA lncrna 54 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0104_chr2-156319615-156320997.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000634100 sg00000282440 ac074099.1-201 2 156305108 156320255 - lnc_RNA lncrna 3 | 9124 enst00000406048 sg00000153234 nr4a2-202 2 156327904 156330121 - mRNA protein_coding 4 | 9710 enst00000409108 sg00000153234 nr4a2-203 2 156325744 156330707 - mRNA protein_coding 5 | 9724 enst00000429376 sg00000153234 nr4a2-210 2 156325744 156330721 - mRNA protein_coding 6 | 9791 enst00000417764 sg00000153234 nr4a2-205 2 156325100 156330788 - mRNA nonsense_mediated_decay 7 | 10968 enst00000417972 sg00000153234 nr4a2-206 2 156325100 156331965 - mRNA nonsense_mediated_decay 8 | 11716 enst00000424077 sg00000153234 nr4a2-208 2 156329413 156332713 - mRNA protein_coding 9 | 11717 enst00000426264 sg00000153234 nr4a2-209 2 156325082 156332714 - mRNA protein_coding 10 | 11723 enst00000421709 sg00000153234 nr4a2-207 2 156329678 156332720 - mRNA protein_coding 11 | 11724 enst00000339562 sg00000153234 nr4a2-201 2 156324437 156332721 - mRNA protein_coding 12 | 21351 enst00000409572 sg00000153234 nr4a2-204 2 156325098 156342348 - mRNA protein_coding 13 | -64665 enst00000637554 sg00000226383 linc01876-207 2 156021751 156254950 - lnc_RNA lncrna 14 | -64665 enst00000636956 sg00000226383 linc01876-204 2 156021751 156254950 - lnc_RNA lncrna 15 | -64673 enst00000659502 sg00000226383 linc01876-211 2 156020540 156254942 - lnc_RNA lncrna 16 | -64679 enst00000428651 sg00000226383 linc01876-201 2 156020540 156254936 - lnc_RNA lncrna 17 | -64680 enst00000661513 sg00000226383 linc01876-212 2 156020540 156254935 - lnc_RNA lncrna 18 | -64681 enst00000657334 sg00000226383 linc01876-210 2 156020540 156254934 - lnc_RNA lncrna 19 | -64684 enst00000637324 sg00000226383 linc01876-205 2 156022781 156254931 - lnc_RNA lncrna 20 | -64686 enst00000635799 sg00000226383 linc01876-203 2 156011530 156254929 - lnc_RNA lncrna 21 | -64697 enst00000638047 sg00000226383 linc01876-209 2 156020540 156254918 - lnc_RNA lncrna 22 | -64697 enst00000662073 sg00000226383 linc01876-213 2 156020535 156254918 - lnc_RNA lncrna 23 | -64700 enst00000637665 sg00000226383 linc01876-208 2 156021761 156254915 - lnc_RNA lncrna 24 | -64710 enst00000637476 sg00000226383 linc01876-206 2 156022686 156254905 - lnc_RNA lncrna 25 | 114293 enst00000415049 sg00000115159 gpd2-205 2 156435290 156510849 + mRNA protein_coding 26 | 114444 enst00000310454 sg00000115159 gpd2-201 2 156435441 156586403 + mRNA protein_coding 27 | 115382 enst00000438166 sg00000115159 gpd2-208 2 156436379 156586403 + mRNA protein_coding 28 | 115430 enst00000495851 sg00000115159 gpd2-211 2 156436427 156501881 + lnc_RNA processed_transcript 29 | 115488 enst00000540309 sg00000115159 gpd2-213 2 156436485 156583404 + mRNA protein_coding 30 | 152575 enst00000409861 sg00000115159 gpd2-204 2 156473572 156613735 + mRNA nonsense_mediated_decay 31 | 152575 enst00000409125 sg00000115159 gpd2-202 2 156473572 156583228 + mRNA protein_coding 32 | 152575 enst00000409674 sg00000115159 gpd2-203 2 156473572 156583058 + mRNA protein_coding 33 | 152575 enst00000416888 sg00000115159 gpd2-206 2 156473572 156501844 + mRNA nonsense_mediated_decay 34 | 152595 enst00000430992 sg00000115159 gpd2-207 2 156473592 156510834 + mRNA nonsense_mediated_decay 35 | 250175 enst00000464846 sg00000115159 gpd2-209 2 156571172 156583009 + lnc_RNA retained_intron 36 | 258086 enst00000492005 sg00000115159 gpd2-210 2 156579083 156583048 + lnc_RNA processed_transcript 37 | 258689 enst00000496190 sg00000115159 gpd2-212 2 156579686 156583273 + lnc_RNA processed_transcript 38 | -285535 enst00000450741 sg00000235548 ac073551.1-201 2 156033247 156034080 - pseudogenic_transcript processed_pseudogene 39 | -295002 enst00000448255 sg00000226383 linc01876-202 2 156011617 156024613 - lnc_RNA lncrna 40 | 334227 enst00000637749 sg00000283436 linc01958-201 2 156655224 156695659 + lnc_RNA lncrna 41 | 457375 enst00000416050 sg00000238069 rplp0p7-201 2 156777706 156778372 - pseudogenic_transcript processed_pseudogene 42 | 467734 enst00000665531 sg00000287048 ac096589.2-201 2 156788731 156865701 + lnc_RNA lncrna 43 | 482342 enst00000670545 sg00000286889 ac096589.1-201 2 156803339 156891160 + lnc_RNA lncrna 44 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0105_chr12-80707849-80709118.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -215 enst00000228641 sg00000111046 myf6-201 12 80707634 80709474 + mRNA protein_coding 3 | 7794 enst00000228644 sg00000111049 myf5-201 12 80716912 80719671 + mRNA protein_coding 4 | 54033 enst00000655211 sg00000257741 linc01490-205 12 80763151 80770331 + lnc_RNA lncrna 5 | 54036 enst00000551399 sg00000257741 linc01490-202 12 80763154 80770717 + lnc_RNA lncrna 6 | 54036 enst00000548705 sg00000257741 linc01490-201 12 80763154 80769891 + lnc_RNA lncrna 7 | 54037 enst00000669331 sg00000257741 linc01490-211 12 80763155 80770717 + lnc_RNA lncrna 8 | 54039 enst00000663278 sg00000257741 linc01490-208 12 80763157 80770717 + lnc_RNA lncrna 9 | 54072 enst00000653991 sg00000257741 linc01490-204 12 80763190 80770311 + lnc_RNA lncrna 10 | 54075 enst00000653130 sg00000257741 linc01490-203 12 80763193 80767627 + lnc_RNA lncrna 11 | 54077 enst00000658715 sg00000257741 linc01490-207 12 80763195 80770301 + lnc_RNA lncrna 12 | 54077 enst00000668136 sg00000257741 linc01490-210 12 80763195 80770301 + lnc_RNA lncrna 13 | 54085 enst00000656352 sg00000257741 linc01490-206 12 80763203 80770301 + lnc_RNA lncrna 14 | 54092 enst00000664923 sg00000257741 linc01490-209 12 80763210 80770301 + lnc_RNA lncrna 15 | -73179 enst00000549355 sg00000139304 ptprq-204 12 80634670 80652824 + lnc_RNA retained_intron 16 | -75627 enst00000547881 sg00000139304 ptprq-203 12 80632222 80658051 + mRNA protein_coding 17 | -114148 enst00000550634 sg00000257429 ac074031.1-201 12 80583683 80593701 - lnc_RNA lncrna 18 | 123511 enst00000385030 sg00000207763 mir617-201 12 80832533 80832629 - miRNA mirna 19 | -146289 enst00000547384 sg00000257786 akirin1p1-201 12 80561017 80561560 - pseudogenic_transcript processed_pseudogene 20 | 152390 enst00000549144 sg00000258215 ac078886.1-201 12 80860955 80861508 - pseudogenic_transcript processed_pseudogene 21 | -165593 enst00000551624 sg00000139304 ptprq-207 12 80542256 80547123 + lnc_RNA retained_intron 22 | 180230 enst00000552093 sg00000111052 lin7a-203 12 80845564 80889348 - mRNA protein_coding 23 | -195207 enst00000547485 sg00000139304 ptprq-202 12 80512642 80539838 + lnc_RNA processed_transcript 24 | 226715 enst00000385287 sg00000208022 mir618-201 12 80935736 80935833 - miRNA mirna 25 | 227296 enst00000616449 sg00000111058 acss3-208 12 80936414 80940246 + lnc_RNA processed_transcript 26 | 228586 enst00000549417 sg00000111052 lin7a-202 12 80841689 80937704 - mRNA protein_coding 27 | 228662 enst00000261203 sg00000111052 lin7a-201 12 80797575 80937780 - mRNA nonsense_mediated_decay 28 | 228697 enst00000549175 sg00000111058 acss3-206 12 80937815 81134963 + mRNA protein_coding 29 | 228741 enst00000650935 sg00000111058 acss3-209 12 80937859 80951061 + lnc_RNA processed_transcript 30 | 228807 enst00000552864 sg00000111052 lin7a-204 12 80792520 80937925 - mRNA protein_coding 31 | 234928 enst00000651903 sg00000111058 acss3-210 12 80944046 80949589 + lnc_RNA processed_transcript 32 | -263614 enst00000644991 sg00000139304 ptprq-210 12 80444235 80680273 + mRNA protein_coding 33 | -272766 enst00000616559 sg00000139304 ptprq-208 12 80435083 80680189 + mRNA protein_coding 34 | -287092 enst00000551573 sg00000139304 ptprq-206 12 80420757 80445524 + mRNA protein_coding 35 | -287096 enst00000547376 sg00000139304 ptprq-201 12 80420753 80445524 + mRNA protein_coding 36 | -301855 enst00000551042 sg00000139304 ptprq-205 12 80405994 80445717 + mRNA protein_coding 37 | -305671 enst00000623635 sg00000139304 ptprq-209 12 80402178 80409550 + lnc_RNA processed_transcript 38 | -340148 enst00000550182 sg00000165899 otogl-205 12 80367701 80370838 + mRNA protein_coding 39 | -349560 enst00000642294 sg00000165899 otogl-207 12 80358289 80378756 + mRNA nonsense_mediated_decay 40 | -351367 enst00000551340 sg00000165899 otogl-206 12 80356482 80378859 + mRNA nonsense_mediated_decay 41 | -351495 enst00000546620 sg00000165899 otogl-203 12 80356354 80379090 + lnc_RNA retained_intron 42 | -364057 enst00000410948 sg00000222880 rn7skp261-201 12 80343515 80343792 - ncRNA misc_rna 43 | 368939 enst00000261206 sg00000111058 acss3-201 12 81078057 81255466 + mRNA protein_coding 44 | 368961 enst00000548058 sg00000111058 acss3-203 12 81078079 81261210 + mRNA protein_coding 45 | -371337 enst00000298820 sg00000165899 otogl-201 12 80336512 80379079 + mRNA protein_coding 46 | 416727 enst00000547123 sg00000258026 ac078955.1-201 12 81094375 81125845 - lnc_RNA lncrna 47 | 416745 enst00000653205 sg00000258026 ac078955.1-202 12 81094371 81125863 - lnc_RNA lncrna 48 | 425677 enst00000548387 sg00000111058 acss3-205 12 81134795 81143502 + lnc_RNA retained_intron 49 | 442533 enst00000548324 sg00000111058 acss3-204 12 81151651 81255803 + lnc_RNA retained_intron 50 | 449270 enst00000578957 sg00000265227 mir4699-201 12 81158388 81158461 + miRNA mirna 51 | 465440 enst00000551745 sg00000111058 acss3-207 12 81174558 81199822 + lnc_RNA retained_intron 52 | 465714 enst00000546664 sg00000111058 acss3-202 12 81174832 81220031 + mRNA nonsense_mediated_decay 53 | -498396 enst00000458043 sg00000165899 otogl-202 12 80209453 80379090 + mRNA protein_coding 54 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0113_chr1-18482252-18483305.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -1270 enst00000400664 sg00000179023 klhdc7a-201 1 18480982 18486126 + mRNA protein_coding 3 | 29813 enst00000596113 sg00000235282 dynll1p3-201 1 18513118 18513383 + pseudogenic_transcript processed_pseudogene 4 | -96423 enst00000420211 sg00000225387 al591896.1-201 1 18385829 18388514 + lnc_RNA lncrna 5 | -106295 enst00000473951 sg00000117154 igsf21-203 1 18375957 18376920 + lnc_RNA processed_transcript 6 | 112109 enst00000450125 sg00000225478 al031737.1-201 1 18595414 18595636 + pseudogenic_transcript processed_pseudogene 7 | -120885 enst00000497331 sg00000117154 igsf21-204 1 18361367 18378483 + lnc_RNA retained_intron 8 | 147541 enst00000420770 sg00000009709 pax7-203 1 18630846 18748866 + mRNA protein_coding 9 | 147701 enst00000375375 sg00000009709 pax7-201 1 18631006 18736138 + mRNA protein_coding 10 | 148219 enst00000400661 sg00000009709 pax7-202 1 18631524 18736102 + mRNA protein_coding 11 | -203407 enst00000412684 sg00000117154 igsf21-202 1 18278845 18376367 + lnc_RNA processed_transcript 12 | -302906 enst00000419667 sg00000230035 igsf21-as1-201 1 18166929 18179346 - lnc_RNA lncrna 13 | -372863 enst00000624418 sg00000280222 al365209.1-201 1 18109389 18115861 + unconfirmed_transcript tec 14 | -374454 enst00000251296 sg00000117154 igsf21-201 1 18107798 18378483 + mRNA protein_coding 15 | 376377 enst00000375371 sg00000179002 tas1r2-201 1 18839599 18859682 - mRNA protein_coding 16 | 399970 enst00000577305 sg00000265606 mir4695-201 1 18883202 18883275 - miRNA mirna 17 | 402314 enst00000454547 sg00000159423 aldh4a1-204 1 18882560 18885619 - lnc_RNA processed_transcript 18 | 407586 enst00000538309 sg00000159423 aldh4a1-205 1 18872733 18890891 - mRNA protein_coding 19 | 413843 enst00000408735 sg00000221662 mir1290-201 1 18897071 18897148 - miRNA mirna 20 | -416595 enst00000569711 sg00000261781 linc01654-201 1 18065657 18074412 + lnc_RNA lncrna 21 | 419223 enst00000538839 sg00000159423 aldh4a1-206 1 18871432 18902528 - mRNA protein_coding 22 | 419248 enst00000290597 sg00000159423 aldh4a1-201 1 18871430 18902553 - mRNA protein_coding 23 | 419250 enst00000375341 sg00000159423 aldh4a1-202 1 18871430 18902555 - mRNA protein_coding 24 | 419419 enst00000432718 sg00000159423 aldh4a1-203 1 18883111 18902724 - mRNA protein_coding 25 | 428687 enst00000355609 sg00000169991 iffo2-201 1 18908291 18911992 - mRNA protein_coding 26 | -466540 enst00000641892 sg00000284653 al357509.1-201 1 18015712 18045612 + lnc_RNA lncrna 27 | 472393 enst00000416166 sg00000169991 iffo2-202 1 18908340 18955698 - mRNA protein_coding 28 | 473371 enst00000455833 sg00000169991 iffo2-203 1 18904280 18956676 - mRNA protein_coding 29 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0117_chr1-217137129-217138574.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000366940 sg00000196482 esrrg-207 1 216503251 217137755 - mRNA protein_coding 3 | 0 enst00000493603 sg00000196482 esrrg-221 1 216503254 217137754 - mRNA protein_coding 4 | -46582 enst00000488947 sg00000196482 esrrg-220 1 216865061 217090547 - lnc_RNA processed_transcript 5 | -47323 enst00000673908 sg00000196482 esrrg-225 1 216503255 217089806 - mRNA protein_coding 6 | -47484 enst00000361525 sg00000196482 esrrg-204 1 216503246 217089645 - mRNA protein_coding 7 | -47493 enst00000471371 sg00000196482 esrrg-215 1 216862230 217089636 - lnc_RNA processed_transcript 8 | -47516 enst00000459825 sg00000196482 esrrg-210 1 216865117 217089613 - lnc_RNA processed_transcript 9 | -47524 enst00000359162 sg00000196482 esrrg-201 1 216503254 217089605 - mRNA protein_coding 10 | -58769 enst00000477799 sg00000196482 esrrg-217 1 216855042 217078360 - lnc_RNA processed_transcript 11 | -58841 enst00000586199 sg00000196482 esrrg-223 1 216567988 217078288 - mRNA nonsense_mediated_decay 12 | -60198 enst00000463665 sg00000196482 esrrg-212 1 216505454 217076931 - mRNA protein_coding 13 | -60240 enst00000493748 sg00000196482 esrrg-222 1 216506788 217076889 - mRNA protein_coding 14 | -197456 enst00000361395 sg00000196482 esrrg-203 1 216503254 216939673 - mRNA protein_coding 15 | -197456 enst00000366938 sg00000196482 esrrg-206 1 216503254 216939673 - mRNA protein_coding 16 | -197459 enst00000487276 sg00000196482 esrrg-219 1 216505490 216939670 - mRNA protein_coding 17 | -331762 enst00000360012 sg00000196482 esrrg-202 1 216503254 216805367 - mRNA protein_coding 18 | 360190 enst00000489246 sg00000092978 gpatch2-205 1 217491506 217498764 - lnc_RNA processed_transcript 19 | -413657 enst00000391890 sg00000196482 esrrg-208 1 216503246 216723472 - mRNA protein_coding 20 | -413676 enst00000366937 sg00000196482 esrrg-205 1 216503254 216723453 - mRNA protein_coding 21 | -413677 enst00000459955 sg00000196482 esrrg-211 1 216677312 216723452 - mRNA protein_coding 22 | -413700 enst00000469913 sg00000196482 esrrg-214 1 216707420 216723429 - lnc_RNA processed_transcript 23 | -413700 enst00000408911 sg00000196482 esrrg-209 1 216503251 216723429 - mRNA protein_coding 24 | -413704 enst00000481543 sg00000196482 esrrg-218 1 216677328 216723425 - mRNA protein_coding 25 | -413713 enst00000469486 sg00000196482 esrrg-213 1 216677201 216723416 - mRNA protein_coding 26 | -413797 enst00000475275 sg00000196482 esrrg-216 1 216519152 216723332 - mRNA protein_coding 27 | -421876 enst00000616180 sg00000196482 esrrg-224 1 216503246 216715253 - mRNA protein_coding 28 | 471805 enst00000485274 sg00000092978 gpatch2-204 1 217498180 217610379 - lnc_RNA processed_transcript 29 | 471826 enst00000470014 sg00000092978 gpatch2-203 1 217492501 217610400 - lnc_RNA processed_transcript 30 | 492508 enst00000366934 sg00000092978 gpatch2-201 1 217608184 217631082 - mRNA protein_coding 31 | 492516 enst00000366935 sg00000092978 gpatch2-202 1 217426992 217631090 - mRNA protein_coding 32 | 492750 enst00000470448 sg00000162814 spata17-202 1 217631324 217774424 + mRNA nonsense_mediated_decay 33 | 492770 enst00000366933 sg00000162814 spata17-201 1 217631344 217871696 + mRNA protein_coding 34 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0128_chr5-11384413-11385577.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 enst00000495388 sg00000169862 ctnnd2-203 5 10972532 11384771 - lnc_RNA processed_transcript 3 | 0 enst00000506735 sg00000169862 ctnnd2-209 5 11346595 11384912 - lnc_RNA processed_transcript 4 | 0 enst00000507430 sg00000169862 ctnnd2-210 5 11364598 11384937 - lnc_RNA retained_intron 5 | 434 enst00000514132 sg00000169862 ctnnd2-217 5 11384982 11386011 - lnc_RNA processed_transcript 6 | 203234 enst00000513598 sg00000169862 ctnnd2-216 5 11385025 11588811 - mRNA protein_coding 7 | 203271 enst00000503622 sg00000169862 ctnnd2-205 5 10973340 11588848 - mRNA protein_coding 8 | 203271 enst00000504354 sg00000169862 ctnnd2-206 5 11346428 11588848 - lnc_RNA processed_transcript 9 | 203442 enst00000511377 sg00000169862 ctnnd2-214 5 10972895 11589019 - mRNA protein_coding 10 | -266921 enst00000458100 sg00000169862 ctnnd2-202 5 10972933 11117492 - mRNA protein_coding 11 | -357213 enst00000384582 sg00000207312 rnu6-429p-201 5 11027200 11027307 + snRNA snrna 12 | -366353 enst00000506324 sg00000169862 ctnnd2-208 5 10973587 11018060 - lnc_RNA processed_transcript 13 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0135_chr20-40682660-40683906.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 5330 enst00000373313 sg00000204103 mafb-201 20 40685848 40689236 - mRNA protein_coding 3 | 14710 enst00000428495 sg00000229771 al035665.1-201 20 40696499 40698616 - lnc_RNA lncrna 4 | 33351 enst00000655799 sg00000286972 al035665.2-201 20 40717257 40758636 + lnc_RNA lncrna 5 | 170323 enst00000458857 sg00000238908 rna5sp484-201 20 40854119 40854229 - pseudogenic_transcript rrna_pseudogene 6 | 340299 enst00000410680 sg00000222612 rnu2-52p-201 20 41024205 41024394 + snRNA snrna 7 | 344916 enst00000361337 sg00000198900 top1-201 20 41028822 41124487 + mRNA protein_coding 8 | 453054 enst00000244007 sg00000124181 plcg1-201 20 41136960 41175721 + mRNA protein_coding 9 | 453179 enst00000660264 sg00000226648 plcg1-as1-202 20 41130658 41137085 - lnc_RNA lncrna 10 | 453179 enst00000667669 sg00000226648 plcg1-as1-205 20 41129996 41137085 - lnc_RNA lncrna 11 | 453179 enst00000661983 sg00000226648 plcg1-as1-203 20 41098417 41137085 - lnc_RNA lncrna 12 | 453179 enst00000669288 sg00000226648 plcg1-as1-206 20 41098019 41137085 - lnc_RNA lncrna 13 | 453331 enst00000373271 sg00000124181 plcg1-202 20 41137237 41177626 + mRNA protein_coding 14 | 453644 enst00000490253 sg00000124181 plcg1-211 20 41137550 41159823 + lnc_RNA retained_intron 15 | 453826 enst00000483646 sg00000124181 plcg1-210 20 41137732 41162647 + lnc_RNA processed_transcript 16 | 454076 enst00000662554 sg00000226648 plcg1-as1-204 20 41109501 41137982 - lnc_RNA lncrna 17 | 454097 enst00000454626 sg00000226648 plcg1-as1-201 20 41098329 41138003 - lnc_RNA lncrna 18 | 479056 enst00000492148 sg00000124181 plcg1-212 20 41162962 41163982 + lnc_RNA retained_intron 19 | 479268 enst00000470528 sg00000124181 plcg1-206 20 41163174 41164005 + lnc_RNA retained_intron 20 | 481374 enst00000473632 sg00000124181 plcg1-207 20 41165280 41165860 + lnc_RNA retained_intron 21 | 481901 enst00000465571 sg00000124181 plcg1-205 20 41165807 41166880 + lnc_RNA retained_intron 22 | 482822 enst00000617873 sg00000124181 plcg1-220 20 41166728 41169628 + lnc_RNA processed_transcript 23 | 483751 enst00000477870 sg00000124181 plcg1-208 20 41167657 41170618 + lnc_RNA retained_intron 24 | 484010 enst00000483175 sg00000124181 plcg1-209 20 41167916 41170910 + lnc_RNA retained_intron 25 | 484893 enst00000619272 sg00000124181 plcg1-221 20 41168799 41170251 + lnc_RNA processed_transcript 26 | 484935 enst00000612731 sg00000124181 plcg1-219 20 41168841 41176281 + mRNA protein_coding 27 | 485117 enst00000613433 sg00000276169 mir6871-201 20 41169023 41169078 + miRNA mirna 28 | 486283 enst00000599785 sg00000124181 plcg1-213 20 41170189 41182989 + mRNA nonsense_mediated_decay 29 | 488505 enst00000461641 sg00000124181 plcg1-204 20 41172411 41174312 + lnc_RNA retained_intron 30 | 488533 enst00000608689 sg00000124181 plcg1-215 20 41172439 41182989 + lnc_RNA processed_transcript 31 | 488610 enst00000608885 sg00000124181 plcg1-216 20 41172516 41182989 + mRNA nonsense_mediated_decay 32 | 489601 enst00000609821 sg00000124181 plcg1-218 20 41173507 41182960 + lnc_RNA processed_transcript 33 | 489825 enst00000609257 sg00000124181 plcg1-217 20 41173731 41182960 + mRNA nonsense_mediated_decay 34 | 489898 enst00000607954 sg00000124181 plcg1-214 20 41173804 41182989 + mRNA nonsense_mediated_decay 35 | 496550 enst00000423733 sg00000124181 plcg1-203 20 41180456 41196787 + lnc_RNA processed_transcript 36 | 496629 enst00000630423 sg00000124181 plcg1-222 20 41180535 41196801 + lnc_RNA processed_transcript 37 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0136_chr8-902134-903249.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -9022 enst00000633456 sg00000282759 ac026950.2-201 8 891251 893112 - lnc_RNA lncrna 3 | -18806 enst00000578889 sg00000198010 dlgap2-213 8 883328 1105066 + lnc_RNA processed_transcript 4 | -18936 enst00000524139 sg00000198010 dlgap2-211 8 883198 1032931 + lnc_RNA processed_transcript 5 | -79955 enst00000421627 sg00000198010 dlgap2-201 8 822179 1701406 + mRNA protein_coding 6 | 115508 enst00000634128 sg00000282692 ac129915.3-201 8 1018757 1019704 + lnc_RNA lncrna 7 | -163586 enst00000631653 sg00000282375 ac100797.5-201 8 738548 740374 + lnc_RNA lncrna 8 | -164028 enst00000518277 sg00000104714 erich1-202 8 673865 738106 - lnc_RNA processed_transcript 9 | -164392 enst00000577187 sg00000198010 dlgap2-212 8 737742 910575 + lnc_RNA processed_transcript 10 | -164470 enst00000520816 sg00000198010 dlgap2-204 8 737664 754258 + lnc_RNA processed_transcript 11 | -164483 enst00000522092 sg00000198010 dlgap2-206 8 737651 1137777 + lnc_RNA processed_transcript 12 | -164538 enst00000637795 sg00000198010 dlgap2-215 8 737596 1701406 + mRNA protein_coding 13 | -170910 enst00000262109 sg00000104714 erich1-201 8 664200 731224 - mRNA protein_coding 14 | -170937 enst00000522706 sg00000104714 erich1-206 8 614746 731197 - mRNA protein_coding 15 | -176257 enst00000520760 sg00000254207 ac100797.1-201 8 725188 725877 - lnc_RNA lncrna 16 | -186207 enst00000524138 sg00000104714 erich1-211 8 673767 715927 - lnc_RNA processed_transcript 17 | 201633 enst00000520524 sg00000198010 dlgap2-203 8 1104882 1262580 + lnc_RNA processed_transcript 18 | -215410 enst00000518313 sg00000104714 erich1-203 8 673844 686724 - lnc_RNA processed_transcript 19 | -228477 enst00000522893 sg00000104714 erich1-207 8 665992 673657 - mRNA protein_coding 20 | -228672 enst00000518895 sg00000104714 erich1-204 8 671794 673462 - lnc_RNA processed_transcript 21 | -228808 enst00000523415 sg00000104714 erich1-209 8 614749 673326 - mRNA nonsense_mediated_decay 22 | -232857 enst00000523053 sg00000104714 erich1-208 8 664622 669277 - lnc_RNA retained_intron 23 | -260927 enst00000523709 sg00000104714 erich1-210 8 637536 641207 - lnc_RNA processed_transcript 24 | -261502 enst00000519909 sg00000104714 erich1-205 8 616526 640632 - lnc_RNA processed_transcript 25 | 345511 enst00000517950 sg00000254160 ac110288.1-201 8 1246789 1248760 - lnc_RNA lncrna 26 | 347124 enst00000522989 sg00000198010 dlgap2-209 8 1250373 1262580 + lnc_RNA processed_transcript 27 | 356330 enst00000522626 sg00000198010 dlgap2-208 8 1259579 1262580 + lnc_RNA retained_intron 28 | -356353 enst00000523656 sg00000180190 tdrp-203 8 489803 545781 - mRNA protein_coding 29 | -356353 enst00000613071 sg00000180190 tdrp-205 8 489792 545781 - mRNA protein_coding 30 | -357136 enst00000324079 sg00000180190 tdrp-201 8 489803 544998 - mRNA protein_coding 31 | -357289 enst00000427263 sg00000180190 tdrp-202 8 489792 544845 - mRNA protein_coding 32 | 399358 enst00000617093 sg00000275427 af067845.2-201 8 1296034 1302607 - lnc_RNA lncrna 33 | -407124 enst00000524229 sg00000180190 tdrp-204 8 492630 495010 - lnc_RNA processed_transcript 34 | -413622 enst00000623988 sg00000279852 ac083964.2-201 8 486117 488512 - unconfirmed_transcript tec 35 | -433419 enst00000519274 sg00000147364 fbxo25-207 8 468715 471225 + mRNA nonsense_mediated_decay 36 | -443624 enst00000517464 sg00000147364 fbxo25-205 8 458510 468180 + lnc_RNA retained_intron 37 | -443765 enst00000519376 sg00000147364 fbxo25-208 8 458369 468014 + lnc_RNA processed_transcript 38 | -450791 enst00000607549 sg00000272293 ac083964.1-201 8 450714 451343 - lnc_RNA lncrna 39 | 466584 enst00000567210 sg00000260721 af067845.1-201 8 1368642 1369833 - lnc_RNA lncrna 40 | -466686 enst00000524015 sg00000147364 fbxo25-209 8 435448 451380 + lnc_RNA retained_intron 41 | 470436 enst00000633906 sg00000282160 af067845.5-201 8 1373685 1381394 + lnc_RNA lncrna 42 | 474618 enst00000633198 sg00000281961 af067845.4-201 8 1377867 1380307 + lnc_RNA lncrna 43 | -481737 enst00000524125 sg00000147364 fbxo25-210 8 420397 451320 + lnc_RNA processed_transcript 44 | -489062 enst00000276326 sg00000147364 fbxo25-201 8 413072 469873 + mRNA protein_coding 45 | -495179 enst00000382824 sg00000147364 fbxo25-204 8 406955 477967 + mRNA protein_coding 46 | -495326 enst00000352684 sg00000147364 fbxo25-203 8 406808 469871 + mRNA protein_coding 47 | -495326 enst00000350302 sg00000147364 fbxo25-202 8 406808 469690 + mRNA protein_coding 48 | -495706 enst00000518240 sg00000147364 fbxo25-206 8 406428 435700 + mRNA protein_coding 49 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0147_chr2-44944047-44945194.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -2174 enst00000419364 sg00000236502 six3-as1-201 2 44940154 44941873 - lnc_RNA lncrna 3 | -2345 enst00000260653 sg00000138083 six3-201 2 44941702 44946071 + mRNA protein_coding 4 | -2553 enst00000456467 sg00000236502 six3-as1-202 2 44940584 44941494 - lnc_RNA lncrna 5 | -4002 enst00000621512 sg00000276670 ac012354.7-201 2 44940045 44940245 + ncRNA misc_rna 6 | -4848 enst00000437916 sg00000259439 linc01833-203 2 44921077 44939199 - lnc_RNA lncrna 7 | -5159 enst00000444871 sg00000259439 linc01833-204 2 44931122 44938888 - lnc_RNA lncrna 8 | -5214 enst00000620790 sg00000274547 ac012354.4-201 2 44938833 44939028 + ncRNA misc_rna 9 | -6621 enst00000611000 sg00000276048 ac012354.5-201 2 44937426 44937696 + ncRNA misc_rna 10 | -8403 enst00000432125 sg00000259439 linc01833-202 2 44923035 44935644 - lnc_RNA lncrna 11 | -8462 enst00000615706 sg00000277809 ac012354.9-201 2 44935585 44935908 + ncRNA misc_rna 12 | -8688 enst00000430847 sg00000259439 linc01833-201 2 44929977 44935359 - lnc_RNA lncrna 13 | -8753 enst00000622214 sg00000276229 ac012354.6-201 2 44935294 44935368 + ncRNA misc_rna 14 | 9470 enst00000425325 sg00000225156 ac012354.1-201 2 44954664 44968762 + lnc_RNA lncrna 15 | -9992 enst00000616963 sg00000277311 ac012354.8-201 2 44934055 44934271 + ncRNA misc_rna 16 | -11727 enst00000620900 sg00000274520 ac012354.3-201 2 44932320 44932406 + ncRNA misc_rna 17 | -15651 enst00000623734 sg00000278957 ac012354.10-201 2 44927914 44928396 - unconfirmed_transcript tec 18 | -21008 enst00000560399 sg00000259439 linc01833-205 2 44921077 44923039 - lnc_RNA lncrna 19 | 51219 enst00000423051 sg00000231848 ac012354.2-201 2 44996413 44996873 + pseudogenic_transcript processed_pseudogene 20 | 64258 enst00000303077 sg00000170577 six2-201 2 45005182 45009452 - mRNA protein_coding 21 | 68474 enst00000423433 sg00000231156 ac093702.1-201 2 45013214 45013668 - lnc_RNA lncrna 22 | 223389 enst00000442821 sg00000231054 ac093833.1-201 2 45168583 45169414 + lnc_RNA lncrna 23 | 224422 enst00000652791 sg00000286728 ac009236.2-201 2 45169616 45211673 + lnc_RNA lncrna 24 | 228528 enst00000663266 sg00000286519 ac009236.1-201 2 45173722 45175935 + lnc_RNA lncrna 25 | 230017 enst00000413669 sg00000205054 linc01121-202 2 45174340 45175211 - lnc_RNA lncrna 26 | -239762 enst00000613618 sg00000143919 camkmt-210 2 44704285 44772113 + mRNA protein_coding 27 | 247091 enst00000454673 sg00000205054 linc01121-205 2 45187170 45192285 - lnc_RNA retained_intron 28 | -267453 enst00000477830 sg00000143919 camkmt-209 2 44676594 44743657 + lnc_RNA processed_transcript 29 | 309747 enst00000378479 sg00000205054 linc01121-201 2 45174344 45254941 - lnc_RNA lncrna 30 | 378191 enst00000427020 sg00000205054 linc01121-203 2 45164816 45323385 - lnc_RNA lncrna 31 | 378195 enst00000658738 sg00000205054 linc01121-206 2 45164818 45323389 - lnc_RNA lncrna 32 | 378203 enst00000430650 sg00000205054 linc01121-204 2 45191620 45323397 - lnc_RNA lncrna 33 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0162_chr2-236159308-236160358.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -6136 enst00000384322 sg00000207049 ac079135.1-201 2 236153071 236153172 - ncRNA misc_rna 3 | 6971 enst00000465889 sg00000168505 gbx2-202 2 236165734 236167329 - lnc_RNA processed_transcript 4 | 7089 enst00000415226 sg00000233611 ac019068.1-201 2 236167447 236294927 + lnc_RNA lncrna 5 | 7107 enst00000483218 sg00000233611 ac019068.1-202 2 236167465 236214225 + lnc_RNA lncrna 6 | 7651 enst00000551105 sg00000168505 gbx2-203 2 236165729 236168009 - mRNA protein_coding 7 | 8028 enst00000306318 sg00000168505 gbx2-201 2 236165236 236168386 - mRNA protein_coding 8 | 50190 enst00000363875 sg00000200745 rnu1-31p-201 2 236210373 236210548 - snRNA snrna 9 | 54243 enst00000447030 sg00000182177 asb18-203 2 236196058 236214601 - mRNA protein_coding 10 | 81162 enst00000645891 sg00000182177 asb18-206 2 236194872 236241520 - mRNA protein_coding 11 | -87013 enst00000582831 sg00000264676 rn7sl204p-201 2 236072295 236072556 + ncRNA misc_rna 12 | 93813 enst00000469508 sg00000182177 asb18-204 2 236250541 236254171 - lnc_RNA processed_transcript 13 | 103987 enst00000409749 sg00000182177 asb18-201 2 236194872 236264345 - mRNA protein_coding 14 | 104002 enst00000487961 sg00000182177 asb18-205 2 236247329 236264360 - lnc_RNA retained_intron 15 | 104051 enst00000430053 sg00000182177 asb18-202 2 236214754 236264409 - mRNA protein_coding 16 | -113371 enst00000453371 sg00000157985 agap1-209 2 236045937 236125482 + lnc_RNA processed_transcript 17 | -118557 enst00000482882 sg00000157985 agap1-211 2 236040751 236049831 + lnc_RNA retained_intron 18 | -118696 enst00000466575 sg00000157985 agap1-210 2 236040612 236120279 + lnc_RNA retained_intron 19 | -122058 enst00000458845 sg00000238812 rnu7-127p-201 2 236037250 236037311 + snRNA snrna 20 | 171698 enst00000479471 sg00000132321 iqca1-209 2 236324691 236332056 - lnc_RNA retained_intron 21 | 173005 enst00000479783 sg00000132321 iqca1-210 2 236324671 236333363 - lnc_RNA retained_intron 22 | 186393 enst00000409100 sg00000132321 iqca1-203 2 236324653 236346751 - lnc_RNA processed_transcript 23 | 207202 enst00000605740 sg00000270540 ac093915.1-201 2 236367560 236369102 + lnc_RNA lncrna 24 | 230716 enst00000413353 sg00000232893 iqca1-as1-201 2 236391074 236392388 + lnc_RNA lncrna 25 | 248719 enst00000441645 sg00000231546 rpl3p5-201 2 236407846 236409077 - pseudogenic_transcript transcribed_processed_pseudogene 26 | -250466 enst00000418654 sg00000157985 agap1-206 2 235908842 236120246 + mRNA protein_coding 27 | 252533 enst00000467572 sg00000132321 iqca1-208 2 236380613 236412891 - lnc_RNA processed_transcript 28 | -275913 enst00000448025 sg00000157985 agap1-208 2 235883395 236036697 + mRNA protein_coding 29 | -276815 enst00000415070 sg00000228499 tmsb10p1-201 2 235882362 235882493 - pseudogenic_transcript processed_pseudogene 30 | 294753 enst00000465621 sg00000132321 iqca1-207 2 236392329 236455111 - lnc_RNA processed_transcript 31 | 343338 enst00000418802 sg00000132321 iqca1-205 2 236377116 236503696 - mRNA protein_coding 32 | 343339 enst00000431676 sg00000132321 iqca1-206 2 236324147 236503697 - mRNA protein_coding 33 | 347118 enst00000409907 sg00000132321 iqca1-204 2 236324151 236507476 - mRNA protein_coding 34 | 347174 enst00000254653 sg00000132321 iqca1-201 2 236324151 236507532 - mRNA nonsense_mediated_decay 35 | 347177 enst00000309507 sg00000132321 iqca1-202 2 236324147 236507535 - mRNA protein_coding 36 | -375921 enst00000440101 sg00000222007 ac064874.1-202 2 235773855 235783387 - lnc_RNA lncrna 37 | -383514 enst00000409661 sg00000222007 ac064874.1-201 2 235773855 235775794 - lnc_RNA lncrna 38 | 407429 enst00000447924 sg00000144476 ackr3-202 2 236567787 236581097 + mRNA protein_coding 39 | 409467 enst00000272928 sg00000144476 ackr3-201 2 236569825 236582354 + mRNA protein_coding 40 | -450130 enst00000428334 sg00000157985 agap1-207 2 235709178 236131800 + mRNA protein_coding 41 | -450131 enst00000614409 sg00000157985 agap1-212 2 235709177 236131800 + mRNA protein_coding 42 | -450131 enst00000619456 sg00000157985 agap1-213 2 235709177 235852853 + mRNA protein_coding 43 | -489704 enst00000409538 sg00000157985 agap1-205 2 235669604 236126554 + mRNA protein_coding 44 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0163_chr5-159104866-159105808.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 572 enst00000624206 sg00000279204 ac134043.3-201 5 159106380 159108617 + unconfirmed_transcript tec 3 | -4184 enst00000499583 sg00000245812 linc02202-201 5 159100682 159117478 + lnc_RNA lncrna 4 | -4244 enst00000523301 sg00000245812 linc02202-203 5 159100622 159107217 + lnc_RNA lncrna 5 | -4383 enst00000517335 sg00000245812 linc02202-202 5 159100483 159117323 + lnc_RNA lncrna 6 | -4950 enst00000313708 sg00000164330 ebf1-201 5 158695920 159099916 - mRNA protein_coding 7 | -5105 enst00000517373 sg00000164330 ebf1-203 5 158698689 159099761 - mRNA protein_coding 8 | -5109 enst00000518836 sg00000164330 ebf1-205 5 158695920 159099757 - lnc_RNA processed_transcript 9 | -5173 enst00000380654 sg00000164330 ebf1-202 5 158698664 159099693 - mRNA protein_coding 10 | -7243 enst00000523315 sg00000164330 ebf1-209 5 159084666 159097623 - lnc_RNA processed_transcript 11 | -8260 enst00000522192 sg00000164330 ebf1-208 5 158698885 159096606 - lnc_RNA retained_intron 12 | -8496 enst00000519739 sg00000164330 ebf1-206 5 158695920 159096370 - lnc_RNA retained_intron 13 | -31072 enst00000519890 sg00000164330 ebf1-207 5 158695920 159073794 - lnc_RNA retained_intron 14 | 55552 enst00000519985 sg00000145860 rnf145-207 5 159157824 159161360 - lnc_RNA processed_transcript 15 | 55772 enst00000518284 sg00000145860 rnf145-204 5 159157411 159161580 - lnc_RNA processed_transcript 16 | 57220 enst00000518062 sg00000145860 rnf145-203 5 159161141 159163028 - lnc_RNA retained_intron 17 | 68233 enst00000521266 sg00000145860 rnf145-210 5 159161484 159174041 - lnc_RNA processed_transcript 18 | -85737 enst00000523464 sg00000164330 ebf1-210 5 158731044 159019129 - lnc_RNA processed_transcript 19 | 101826 enst00000520638 sg00000145860 rnf145-209 5 159158521 159207634 - mRNA protein_coding 20 | 102018 enst00000274542 sg00000145860 rnf145-201 5 159157409 159207826 - mRNA protein_coding 21 | 102265 enst00000519865 sg00000145860 rnf145-206 5 159157409 159208073 - mRNA protein_coding 22 | 102324 enst00000521606 sg00000145860 rnf145-211 5 159158291 159208132 - mRNA protein_coding 23 | 103743 enst00000424310 sg00000145860 rnf145-202 5 159157409 159209551 - mRNA protein_coding 24 | 103790 enst00000611185 sg00000145860 rnf145-212 5 159157413 159209598 - mRNA protein_coding 25 | 103983 enst00000520548 sg00000145860 rnf145-208 5 159181960 159209791 - lnc_RNA processed_transcript 26 | 104113 enst00000521204 sg00000253256 ac134043.2-201 5 159209921 159248796 + lnc_RNA lncrna 27 | 104245 enst00000518802 sg00000145860 rnf145-205 5 159158299 159210053 - mRNA protein_coding 28 | -119060 enst00000518425 sg00000253456 ac136424.1-201 5 158985806 158987199 + lnc_RNA lncrna 29 | -121860 enst00000522582 sg00000253811 ac136424.2-201 5 158983006 158984789 + lnc_RNA lncrna 30 | 121907 enst00000520323 sg00000253315 linc01932-201 5 159227715 159245127 + lnc_RNA lncrna 31 | 124386 enst00000516649 sg00000252458 ac134043.1-201 5 159230194 159230322 + snoRNA snorna 32 | 157482 enst00000296786 sg00000164332 ublcp1-201 5 159263290 159286036 + mRNA protein_coding 33 | 168580 enst00000521738 sg00000164332 ublcp1-203 5 159274388 159275333 + lnc_RNA retained_intron 34 | 168734 enst00000519276 sg00000164332 ublcp1-202 5 159274542 159286036 + lnc_RNA retained_intron 35 | 204937 enst00000641961 sg00000249738 ac008691.1-201 5 159310745 159312634 + lnc_RNA lncrna 36 | 205125 enst00000521472 sg00000249738 ac008691.1-202 5 159310933 159333182 + lnc_RNA lncrna 37 | 212234 enst00000408674 sg00000221601 rnu4atac2p-201 5 159318042 159318167 + snRNA snrna 38 | 224679 enst00000231228 sg00000113302 il12b-201 5 159314780 159330487 - mRNA protein_coding 39 | 225710 enst00000515337 sg00000249738 ac008691.1-203 5 159331518 159362834 + lnc_RNA lncrna 40 | 226131 enst00000641150 sg00000249738 ac008691.1-204 5 159331939 159416624 + lnc_RNA lncrna 41 | 240292 enst00000635333 sg00000249738 ac008691.1-205 5 159346100 159451999 + lnc_RNA lncrna 42 | 248261 enst00000648969 sg00000249738 ac008691.1-206 5 159354069 159426698 + lnc_RNA lncrna 43 | -264743 enst00000622875 sg00000164330 ebf1-211 5 158695916 158840123 - mRNA protein_coding 44 | 315406 enst00000636261 sg00000249738 ac008691.1-207 5 159421214 159557687 + lnc_RNA lncrna 45 | 360468 enst00000518418 sg00000253298 linc01845-201 5 159448556 159466276 - lnc_RNA lncrna 46 | 360483 enst00000658947 sg00000253298 linc01845-202 5 159458838 159466291 - lnc_RNA lncrna 47 | -396857 enst00000518323 sg00000164330 ebf1-204 5 158698641 158708009 - lnc_RNA processed_transcript 48 | 405879 enst00000637629 sg00000283413 ac008703.1-201 5 159484130 159511687 - lnc_RNA lncrna 49 | 447194 enst00000636819 sg00000249738 ac008691.1-208 5 159553002 159805536 + lnc_RNA lncrna 50 | 447200 enst00000636943 sg00000249738 ac008691.1-209 5 159553008 159557783 + lnc_RNA lncrna 51 | 471038 enst00000642094 sg00000249738 ac008691.1-210 5 159576846 159587991 + lnc_RNA lncrna 52 | 481058 enst00000641685 sg00000249738 ac008691.1-211 5 159586866 159614595 + lnc_RNA lncrna 53 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0181_chr5-3606229-3607148.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -6041 enst00000559410 sg00000259603 ac016595.1-201 5 3596211 3600188 - lnc_RNA lncrna 3 | -10397 enst00000302006 sg00000170549 irx1-201 5 3595832 3601403 + mRNA protein_coding 4 | -70135 enst00000505443 sg00000248118 linc01019-201 5 3417152 3536094 - lnc_RNA lncrna 5 | -74434 enst00000662836 sg00000248118 linc01019-202 5 3357264 3531795 - lnc_RNA lncrna 6 | -102225 enst00000508823 sg00000250716 linc01017-201 5 3496229 3504004 - lnc_RNA lncrna 7 | -153413 enst00000512521 sg00000249830 linc02162-201 5 3452816 3461660 + lnc_RNA lncrna 8 | 406501 enst00000513859 sg00000248962 ac025773.1-201 5 4012708 4013649 - lnc_RNA lncrna 9 | -428366 enst00000652864 sg00000249808 ac091832.1-202 5 3177863 3181487 + lnc_RNA lncrna 10 | -428394 enst00000505396 sg00000249808 ac091832.1-201 5 3177835 3181232 + lnc_RNA lncrna 11 | 434616 enst00000506305 sg00000249994 ac025187.1-201 5 4033713 4041764 - lnc_RNA lncrna 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/interval_tables/interval_0199_chr11-22340923-22341888.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 1089 enst00000534115 sg00000091664 slc17a6-202 11 22342977 22360965 + lnc_RNA retained_intron 3 | -2542 enst00000263160 sg00000091664 slc17a6-201 11 22338381 22379503 + mRNA protein_coding 4 | -2678 enst00000528009 sg00000254768 ac104009.1-201 11 22283730 22338245 - lnc_RNA lncrna 5 | -2699 enst00000530569 sg00000254768 ac104009.1-202 11 22317752 22338224 - lnc_RNA lncrna 6 | -2699 enst00000531304 sg00000254768 ac104009.1-203 11 22319820 22338224 - lnc_RNA lncrna 7 | -2772 enst00000665562 sg00000254768 ac104009.1-204 11 22332507 22338151 - lnc_RNA lncrna 8 | 17589 enst00000648880 sg00000091664 slc17a6-203 11 22359477 22366369 + lnc_RNA retained_intron 9 | 20406 enst00000534543 sg00000254540 ac040936.1-201 11 22361213 22362294 - lnc_RNA lncrna 10 | -70526 enst00000532043 sg00000171714 ano5-202 11 22270397 22278034 + lnc_RNA processed_transcript 11 | -78667 enst00000526935 sg00000255372 ac107886.1-201 11 22261209 22262256 - lnc_RNA lncrna 12 | -147747 enst00000324559 sg00000171714 ano5-201 11 22193176 22283357 + mRNA protein_coding 13 | 150159 enst00000534135 sg00000255323 linc01495-202 11 22445673 22492047 - lnc_RNA lncrna 14 | 150159 enst00000532380 sg00000255323 linc01495-201 11 22445688 22492047 - lnc_RNA lncrna 15 | 150185 enst00000653021 sg00000255323 linc01495-203 11 22445676 22492073 - lnc_RNA lncrna 16 | 150199 enst00000656032 sg00000255357 ac055878.1-202 11 22492087 22510396 + lnc_RNA lncrna 17 | 150224 enst00000531858 sg00000255357 ac055878.1-201 11 22492112 22502846 + lnc_RNA lncrna 18 | -170922 enst00000659342 sg00000287962 ac116534.1-201 11 22010402 22170001 - lnc_RNA lncrna 19 | -227475 enst00000530837 sg00000254820 ac107882.1-201 11 22113448 22117001 + lnc_RNA lncrna 20 | 283621 enst00000648096 sg00000148935 gas2-211 11 22625509 22626403 + lnc_RNA processed_transcript 21 | 283754 enst00000528582 sg00000148935 gas2-205 11 22625642 22749190 + mRNA protein_coding 22 | 283935 enst00000327470 sg00000183161 fancf-201 11 22622533 22625823 - mRNA protein_coding 23 | 324695 enst00000533092 sg00000148935 gas2-207 11 22666583 22702630 + lnc_RNA processed_transcript 24 | 324727 enst00000454584 sg00000148935 gas2-202 11 22666615 22813055 + mRNA protein_coding 25 | 325188 enst00000533363 sg00000148935 gas2-208 11 22667076 22726432 + mRNA protein_coding 26 | 326220 enst00000630668 sg00000148935 gas2-210 11 22668108 22731347 + mRNA protein_coding 27 | 326220 enst00000278187 sg00000148935 gas2-201 11 22668108 22812996 + mRNA protein_coding 28 | 326220 enst00000524701 sg00000148935 gas2-203 11 22668108 22813001 + mRNA nonsense_mediated_decay 29 | 330689 enst00000534801 sg00000148935 gas2-209 11 22672577 22737760 + mRNA protein_coding 30 | 332885 enst00000532398 sg00000148935 gas2-206 11 22674773 22749261 + mRNA protein_coding 31 | 346463 enst00000410495 sg00000222427 rna5sp338-201 11 22688351 22688435 + pseudogenic_transcript rrna_pseudogene 32 | 413760 enst00000526665 sg00000148935 gas2-204 11 22755648 22755953 + lnc_RNA processed_transcript 33 | 485989 enst00000525670 sg00000198168 svip-202 11 22813799 22827877 - lnc_RNA processed_transcript 34 | 487485 enst00000530199 sg00000198168 svip-204 11 22822867 22829373 - lnc_RNA processed_transcript 35 | 487492 enst00000525963 sg00000246225 ac006299.1-201 11 22829380 22876848 + lnc_RNA lncrna 36 | 487524 enst00000528701 sg00000246225 ac006299.1-202 11 22829412 22922823 + lnc_RNA lncrna 37 | 487526 enst00000663618 sg00000246225 ac006299.1-204 11 22829414 22835491 + lnc_RNA lncrna 38 | 487534 enst00000499625 sg00000246225 ac006299.1-203 11 22829422 22945393 + lnc_RNA lncrna 39 | 487566 enst00000661691 sg00000246225 ac006299.1-205 11 22829454 22885412 + lnc_RNA lncrna 40 | 487683 enst00000533774 sg00000198168 svip-205 11 22822747 22829571 - lnc_RNA processed_transcript 41 | 487913 enst00000354193 sg00000198168 svip-201 11 22818927 22829801 - mRNA protein_coding 42 | 488411 enst00000529848 sg00000198168 svip-203 11 22827245 22830299 - lnc_RNA processed_transcript 43 | -------------------------------------------------------------------------------- /docs/Comp_Report/human_html/out_stdout.txt: -------------------------------------------------------------------------------- 1 | 2 | ------------------------------------------------------------ 3 | Sender: LSF System 4 | Subject: Job 6243079: in cluster Done 5 | 6 | Job was submitted from host by user in cluster at Wed May 20 17:24:00 2020 7 | Job was executed on host(s) <3*hx-noah-13-03>, in queue , as user in cluster at Wed May 20 17:25:45 2020 8 | was used as the home directory. 9 | was used as the working directory. 10 | Started at Wed May 20 17:25:45 2020 11 | Terminated at Wed May 20 17:57:38 2020 12 | Results reported at Wed May 20 17:57:38 2020 13 | 14 | Your job looked like: 15 | 16 | ------------------------------------------------------------ 17 | # LSBATCH: User input 18 | ------------------------------------------------------------ 19 | 20 | Successfully completed. 21 | 22 | Resource usage summary: 23 | 24 | CPU time : 171.60 sec. 25 | Max Memory : 505 MB 26 | Average Memory : 491.93 MB 27 | Total Requested Memory : 20000.00 MB 28 | Delta Memory : 19495.00 MB 29 | Max Swap : 1197 MB 30 | Max Processes : 3 31 | Max Threads : 6 32 | Run time : 1913 sec. 33 | Turnaround time : 2018 sec. 34 | 35 | The output (if any) is above this job summary. 36 | 37 | 38 | 39 | PS: 40 | 41 | Read file for stderr output of this job. 42 | 43 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0001_chr15-13014693-13015794.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000004176 sorlg00000003361 15 13015106 13033440 + mRNA protein_coding 3 | -8498 ensorlt00000045267 sorlg00000003350 ubr2-201 15 13006195 13013991 + mRNA protein_coding 4 | 21564 ensorlt00000037335 sorlg00000003367 kcng3-202 15 13037358 13043655 + mRNA protein_coding 5 | 23467 ensorlt00000004183 sorlg00000003367 kcng3-201 15 13039261 13045301 + mRNA protein_coding 6 | -25121 ensorlt00000004168 sorlg00000003350 ubr2-202 15 12989572 13016886 + mRNA protein_coding 7 | 34372 ensorlt00000004256 sorlg00000003423 tspan14-201 15 13050166 13056192 + mRNA protein_coding 8 | 36681 ensorlt00000004258 sorlg00000003423 tspan14-202 15 13052475 13056192 + mRNA protein_coding 9 | -39845 ensorlt00000029700 sorlg00000025354 si:ch73-193i2.2-201 15 12974848 12988806 + mRNA protein_coding 10 | 41766 ensorlt00000004297 sorlg00000003456 eml4-203 15 13057560 13079758 + mRNA protein_coding 11 | 41766 ensorlt00000045537 sorlg00000003456 eml4-202 15 13057560 13079758 + mRNA protein_coding 12 | 41766 ensorlt00000004296 sorlg00000003456 eml4-201 15 13057560 13079758 + mRNA protein_coding 13 | 41766 ensorlt00000034842 sorlg00000003456 eml4-204 15 13057560 13079758 + mRNA protein_coding 14 | -53337 ensorlt00000037101 sorlg00000029510 prkn-201 15 12961356 12973073 + mRNA protein_coding 15 | -58153 ensorlt00000028644 sorlg00000026680 15 12956540 12960420 + mRNA protein_coding 16 | -59755 ensorlt00000027828 sorlg00000026680 15 12954938 12960420 + mRNA protein_coding 17 | -61142 ensorlt00000041055 sorlg00000026680 15 12953551 12960420 + mRNA protein_coding 18 | 66013 ensorlt00000004302 sorlg00000003462 15 13081310 13081807 - mRNA protein_coding 19 | -70627 ensorlt00000004067 sorlg00000003269 ncoa4-202 15 12944066 12947460 + mRNA protein_coding 20 | -71791 ensorlt00000035874 sorlg00000003269 ncoa4-203 15 12942902 12950436 + mRNA protein_coding 21 | -71791 ensorlt00000038951 sorlg00000003269 ncoa4-201 15 12942902 12950436 + mRNA protein_coding 22 | -74166 ensorlt00000030164 sorlg00000003250 yipf3-201 15 12936661 12940527 - mRNA protein_coding 23 | -74769 ensorlt00000004047 sorlg00000003250 yipf3-202 15 12937188 12939924 - mRNA protein_coding 24 | -78039 ensorlt00000031064 sorlg00000029764 15 12935597 12936654 - mRNA protein_coding 25 | -84441 ensorlt00000039772 sorlg00000026021 15 12930252 12933724 + mRNA protein_coding 26 | -87679 ensorlt00000004007 sorlg00000003216 dnph1-201 15 12926040 12927014 - mRNA protein_coding 27 | -98516 ensorlt00000003996 sorlg00000003209 tjap1-201 15 12916177 12923054 + mRNA protein_coding 28 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0002_chr16-26220047-26221325.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -24958 ensorlt00000019438 sorlg00000015519 sh3bp5b-201 16 26195089 26217510 + mRNA protein_coding 3 | -24958 ensorlt00000028824 sorlg00000015519 sh3bp5b-202 16 26195089 26218930 + mRNA protein_coding 4 | 25471 ensorlt00000019456 sorlg00000015536 capn7-201 16 26236530 26246796 - mRNA protein_coding 5 | 25789 ensorlt00000033538 sorlg00000015536 capn7-202 16 26233651 26247114 - mRNA protein_coding 6 | 30283 ensorlt00000019457 sorlg00000015539 16 26247399 26251608 - mRNA protein_coding 7 | 30860 ensorlt00000034371 sorlg00000025991 16 26252185 26260269 + mRNA protein_coding 8 | -43714 ensorlt00000045098 sorlg00000026772 eaf1-201 16 26168400 26176333 - mRNA protein_coding 9 | -45740 ensorlt00000019426 sorlg00000015510 mettl6-201 16 26174307 26178758 + mRNA protein_coding 10 | -85426 ensorlt00000019395 sorlg00000015488 bmper-202 16 26134621 26167317 + mRNA protein_coding 11 | -88147 ensorlt00000019393 sorlg00000015488 bmper-201 16 26131900 26167317 + mRNA protein_coding 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0003_chr17-316390-318610.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -155 ensorlt00000002667 sorlg00000002147 17 316235 318512 + mRNA protein_coding 3 | 82079 ensorlt00000008553 sorlg00000006808 ccny-202 17 332165 400689 - mRNA protein_coding 4 | 82782 ensorlt00000006032 sorlg00000006808 ccny-201 17 332165 401392 - mRNA protein_coding 5 | 82782 ensorlt00000027208 sorlg00000006808 ccny-203 17 335031 401392 - mRNA protein_coding 6 | 94662 ensorlt00000037733 sorlg00000029136 17 413272 415622 + mRNA protein_coding 7 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0004_chr11-27686928-27688355.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -21358 ensorlt00000017935 sorlg00000014304 11 27665570 27671942 + mRNA protein_coding 3 | 61015 ensorlt00000017944 sorlg00000014310 med10-201 11 27747147 27749370 - mRNA protein_coding 4 | 65156 ensorlt00000034340 sorlg00000025027 11 27750518 27753511 - mRNA protein_coding 5 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0005_chr4-7874048-7875618.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -11370 ensorlt00000006287 sorlg00000004983 onecut3a-201 4 7862678 7878384 + mRNA protein_coding 3 | 20599 ensorlt00000006332 sorlg00000005022 atp8b3-201 4 7878425 7896217 - mRNA protein_coding 4 | 30206 ensorlt00000031831 sorlg00000030341 4 7905824 7912103 + mRNA protein_coding 5 | -39011 ensorlt00000006270 sorlg00000004973 foxq2-201 4 7835037 7837130 + mRNA protein_coding 6 | -41900 ensorlt00000006266 sorlg00000004970 pias4a-201 4 7819692 7832148 - mRNA protein_coding 7 | 54013 ensorlt00000006341 sorlg00000005032 lingo3a-201 4 7927802 7929631 - mRNA protein_coding 8 | -58064 ensorlt00000006224 sorlg00000004940 map2k2a-201 4 7809313 7815984 - mRNA protein_coding 9 | -67885 ensorlt00000046293 sorlg00000028662 zbtb7a-201 4 7798326 7806163 - mRNA protein_coding 10 | -89315 ensorlt00000035303 sorlg00000004923 tcf3b-201 4 7765170 7784733 - mRNA protein_coding 11 | -89337 ensorlt00000006201 sorlg00000004923 tcf3b-202 4 7767436 7784711 - mRNA protein_coding 12 | -89337 ensorlt00000031862 sorlg00000004923 tcf3b-203 4 7767436 7784711 - mRNA protein_coding 13 | 95623 ensorlt00000046472 sorlg00000025930 org-201 4 7965094 7971241 - mRNA protein_coding 14 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0006_chr15-1565040-1565987.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 12910 ensorlt00000023980 sorlg00000019248 galm-201 15 1571975 1578897 - mRNA protein_coding 3 | 21109 ensorlt00000024001 sorlg00000019266 cdk1-201 15 1587096 1590723 + mRNA protein_coding 4 | 30880 ensorlt00000044687 sorlg00000027844 ctu2-202 15 1587096 1596867 - mRNA protein_coding 5 | 31190 ensorlt00000028851 sorlg00000027844 ctu2-201 15 1587096 1597177 - mRNA protein_coding 6 | 38157 ensorlt00000024014 sorlg00000019278 rnf166-201 15 1604144 1613984 + mRNA protein_coding 7 | -47996 ensorlt00000042317 sorlg00000019183 si:dkey-191g9.5-202 15 1517044 1560537 + mRNA protein_coding 8 | 56117 ensorlt00000023962 sorlg00000019226 cyp17-202 15 1615588 1622104 - mRNA protein_coding 9 | 56158 ensorlt00000023960 sorlg00000019226 cyp17-201 15 1614764 1622145 - mRNA protein_coding 10 | 59338 ensorlt00000023957 sorlg00000019226 cyp17-203 15 1615588 1625325 - mRNA protein_coding 11 | 60808 ensorlt00000042626 sorlg00000025880 borcs7-201 15 1626795 1627729 + mRNA protein_coding 12 | -66827 ensorlt00000023904 sorlg00000019183 si:dkey-191g9.5-201 15 1498213 1560537 + mRNA protein_coding 13 | 87404 ensorlt00000043297 sorlg00000028435 15 1648079 1653391 - mRNA protein_coding 14 | 95527 ensorlt00000046918 sorlg00000025269 chchd1-201 15 1661514 1672180 + mRNA protein_coding 15 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0007_chr2-23361417-23362425.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -38910 ensorlt00000007888 sorlg00000006275 gart-201 2 23313034 23322507 - mRNA protein_coding 3 | -68893 ensorlt00000032912 sorlg00000028237 2 23291361 23292524 - mRNA protein_coding 4 | -71227 ensorlt00000007813 sorlg00000006216 2 23286187 23290190 - mRNA protein_coding 5 | -78198 ensorlt00000007807 sorlg00000006210 2 23270364 23283219 - mRNA protein_coding 6 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0008_chr2-12169442-12171060.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -21573 ensorlt00000028404 sorlg00000029493 2 12141322 12147869 - mRNA protein_coding 3 | 74237 ensorlt00000000732 sorlg00000028915 2 12198740 12245297 - mRNA protein_coding 4 | 90821 ensorlt00000000735 sorlg00000027116 2 12256249 12261881 - mRNA protein_coding 5 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0009_chr8-450569-451548.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000033385 sorlg00000030318 8 450353 451492 - mRNA protein_coding 3 | -4733 ensorlt00000029738 sorlg00000024494 8 445836 467574 + mRNA protein_coding 4 | -4928 ensorlt00000045352 sorlg00000024494 8 445641 465188 + mRNA protein_coding 5 | -17401 ensorlt00000034536 sorlg00000019717 8 429256 433168 - mRNA protein_coding 6 | -17755 ensorlt00000024506 sorlg00000019717 8 429256 432814 - mRNA protein_coding 7 | -18149 ensorlt00000040605 sorlg00000019717 8 429077 432420 - mRNA protein_coding 8 | -20052 ensorlt00000041326 sorlg00000026960 8 430517 434408 + mRNA protein_coding 9 | 20145 ensorlt00000023100 sorlg00000018463 8 467358 471693 - mRNA protein_coding 10 | -26338 ensorlt00000024620 sorlg00000019817 8 421326 424231 - mRNA protein_coding 11 | 35466 ensorlt00000044655 sorlg00000030594 rapgefl1-202 8 476240 487014 - mRNA protein_coding 12 | -46989 ensorlt00000039310 sorlg00000023247 8 402245 403580 - mRNA protein_coding 13 | 49252 ensorlt00000033866 sorlg00000030594 rapgefl1-201 8 476240 500800 - mRNA protein_coding 14 | -53129 ensorlt00000025215 sorlg00000020338 8 395496 397440 - mRNA protein_coding 15 | 56818 ensorlt00000044979 sorlg00000023125 casc3-201 8 498727 508366 - mRNA protein_coding 16 | -59481 ensorlt00000027206 sorlg00000028684 si:dkeyp-113d7.1-201 8 391088 397155 + mRNA protein_coding 17 | -61708 ensorlt00000044782 sorlg00000030478 8 388861 390213 + mRNA protein_coding 18 | 64978 ensorlt00000032679 sorlg00000022520 8 516526 517224 + mRNA protein_coding 19 | 68216 ensorlt00000033771 sorlg00000029855 8 510185 519764 - mRNA protein_coding 20 | 71975 ensorlt00000038554 sorlg00000029016 mettl23-201 8 523523 529892 + mRNA protein_coding 21 | 74236 ensorlt00000023115 sorlg00000018477 jmjd6-201 8 522728 525784 - mRNA protein_coding 22 | 74673 ensorlt00000044827 sorlg00000029016 mettl23-202 8 526221 529892 + mRNA protein_coding 23 | 74673 ensorlt00000043485 sorlg00000029016 mettl23-203 8 526221 529484 + mRNA protein_coding 24 | -77441 ensorlt00000028454 sorlg00000030302 8 373128 379718 + mRNA protein_coding 25 | 78864 ensorlt00000035639 sorlg00000026086 8 528250 530412 - mRNA protein_coding 26 | 82159 ensorlt00000032857 sorlg00000023488 caskin2-201 8 533707 562513 + mRNA protein_coding 27 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0010_chr8-23224550-23225428.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -3599 ensorlt00000020885 sorlg00000016693 dnase1-201 8 23220951 23226539 + mRNA protein_coding 3 | 7323 ensorlt00000020895 sorlg00000016704 eci1-201 8 23226933 23232751 - mRNA protein_coding 4 | -7936 ensorlt00000036038 sorlg00000016682 nat15-201 8 23209796 23216614 - mRNA protein_coding 5 | -10397 ensorlt00000020871 sorlg00000016682 nat15-202 8 23209805 23214153 - mRNA protein_coding 6 | 12868 ensorlt00000045455 sorlg00000016708 8 23238296 23245914 + mRNA protein_coding 7 | 14016 ensorlt00000020902 sorlg00000016708 8 23239444 23248941 + mRNA protein_coding 8 | 14016 ensorlt00000035391 sorlg00000016708 8 23239444 23247843 + mRNA protein_coding 9 | 14016 ensorlt00000033670 sorlg00000016708 8 23239444 23248941 + mRNA protein_coding 10 | 14061 ensorlt00000035858 sorlg00000016708 8 23239489 23249852 + mRNA protein_coding 11 | 16127 ensorlt00000040644 sorlg00000016708 8 23241555 23249799 + mRNA protein_coding 12 | -33879 ensorlt00000037447 sorlg00000027715 carhsp1-201 8 23184214 23190671 - mRNA protein_coding 13 | -45525 ensorlt00000020863 sorlg00000016675 8 23157529 23179025 - mRNA protein_coding 14 | 45959 ensorlt00000029013 sorlg00000025723 8 23271387 23274725 + mRNA protein_coding 15 | 45959 ensorlt00000037792 sorlg00000025723 8 23271387 23274725 + mRNA protein_coding 16 | 46393 ensorlt00000032326 sorlg00000025723 8 23271821 23273615 + mRNA protein_coding 17 | -61899 ensorlt00000038325 sorlg00000016675 8 23161828 23162651 - mRNA protein_coding 18 | 73452 ensorlt00000020927 sorlg00000016728 8 23280811 23298880 - mRNA protein_coding 19 | 76148 ensorlt00000029109 sorlg00000016728 8 23276479 23301576 - mRNA protein_coding 20 | 76148 ensorlt00000033402 sorlg00000016728 8 23276479 23301576 - mRNA protein_coding 21 | 77402 ensorlt00000020968 sorlg00000016761 aldh16a1-201 8 23302830 23320952 + mRNA protein_coding 22 | -77528 ensorlt00000020848 sorlg00000016661 prpsap2-202 8 23147022 23152583 + mRNA protein_coding 23 | 78951 ensorlt00000034350 sorlg00000016761 aldh16a1-202 8 23304379 23323108 + mRNA protein_coding 24 | 78951 ensorlt00000037762 sorlg00000016761 aldh16a1-203 8 23304379 23323108 + mRNA protein_coding 25 | -80874 ensorlt00000036035 sorlg00000016661 prpsap2-201 8 23143676 23157508 + mRNA protein_coding 26 | -84642 ensorlt00000029263 sorlg00000016641 caskin1-203 8 23027167 23139908 - mRNA protein_coding 27 | -84642 ensorlt00000042809 sorlg00000016641 caskin1-206 8 23027167 23139908 - mRNA protein_coding 28 | -84642 ensorlt00000039418 sorlg00000016641 caskin1-205 8 23027167 23139908 - mRNA protein_coding 29 | -84642 ensorlt00000020828 sorlg00000016641 caskin1-204 8 23027167 23139908 - mRNA protein_coding 30 | 99228 ensorlt00000020975 sorlg00000027266 8 23324656 23331885 + mRNA protein_coding 31 | 99228 ensorlt00000020971 sorlg00000027266 8 23324656 23340776 + mRNA protein_coding 32 | 99228 ensorlt00000020972 sorlg00000027266 8 23324656 23340776 + mRNA protein_coding 33 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0011_chr2-3660038-3660922.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 1339 ensorlt00000030756 sorlg00000026726 2 3660061 3662261 - mRNA protein_coding 3 | 32942 ensorlt00000000163 sorlg00000000133 sh3bp4a-201 2 3663771 3693864 - mRNA protein_coding 4 | -34679 ensorlt00000000160 sorlg00000000125 aox1-201 2 3599881 3625359 - mRNA protein_coding 5 | 55847 ensorlt00000042213 sorlg00000028907 s100b-201 2 3716769 3719712 + mRNA protein_coding 6 | -65095 ensorlt00000043576 sorlg00000000117 bzw1b-201 2 3582386 3594943 - mRNA protein_coding 7 | 96711 ensorlt00000000166 sorlg00000000135 ahr2-201 2 3757633 3807339 + mRNA protein_coding 8 | -98231 ensorlt00000000142 sorlg00000000115 2 3561807 3575638 + mRNA protein_coding 9 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0012_chr22-1816785-1817685.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 3476 ensorlt00000040061 sorlg00000009716 tc2n-202 22 1821161 1830572 + mRNA protein_coding 3 | 3476 ensorlt00000030930 sorlg00000009716 tc2n-201 22 1821161 1830572 + mRNA protein_coding 4 | 4080 ensorlt00000012187 sorlg00000009716 tc2n-203 22 1821765 1830572 + mRNA protein_coding 5 | 6762 ensorlt00000031580 sorlg00000009716 tc2n-204 22 1824447 1830572 + mRNA protein_coding 6 | -8327 ensorlt00000012170 sorlg00000009701 fbln5-202 22 1808458 1821700 + mRNA protein_coding 7 | -9423 ensorlt00000031737 sorlg00000009701 fbln5-201 22 1807362 1821700 + mRNA protein_coding 8 | 17189 ensorlt00000012211 sorlg00000009734 plek2-201 22 1834874 1838729 + mRNA protein_coding 9 | -28891 ensorlt00000033192 sorlg00000009693 trip11-203 22 1787894 1807185 + mRNA protein_coding 10 | -28891 ensorlt00000039302 sorlg00000009693 trip11-201 22 1787894 1807559 + mRNA protein_coding 11 | -28891 ensorlt00000012156 sorlg00000009693 trip11-202 22 1787894 1807185 + mRNA protein_coding 12 | 29022 ensorlt00000040625 sorlg00000030333 si:ch211-10a23.2-201 22 1838786 1846707 - mRNA protein_coding 13 | 30113 ensorlt00000012353 sorlg00000009842 zfyve26-202 22 1847798 1867855 + mRNA protein_coding 14 | 30113 ensorlt00000012350 sorlg00000009842 zfyve26-201 22 1847798 1867855 + mRNA protein_coding 15 | 31892 ensorlt00000032633 sorlg00000009842 zfyve26-203 22 1849577 1870529 + mRNA protein_coding 16 | -34734 ensorlt00000012149 sorlg00000009684 golga5-201 22 1782051 1787598 + mRNA protein_coding 17 | -41697 ensorlt00000012123 sorlg00000009661 rtf1-203 22 1775088 1780277 + mRNA protein_coding 18 | -47137 ensorlt00000012030 sorlg00000027861 ndufaf1-201 22 1767818 1769648 - mRNA protein_coding 19 | -55722 ensorlt00000012120 sorlg00000009661 rtf1-201 22 1761063 1781813 + mRNA protein_coding 20 | -55722 ensorlt00000012116 sorlg00000009661 rtf1-202 22 1761063 1781813 + mRNA protein_coding 21 | -56965 ensorlt00000012033 sorlg00000024455 ndufaf1-201 22 1757990 1759820 - mRNA protein_coding 22 | 59047 ensorlt00000012384 sorlg00000009869 rdh12-201 22 1870302 1876732 - mRNA protein_coding 23 | 59152 ensorlt00000042124 sorlg00000029032 vti1b-201 22 1876837 1882910 + mRNA protein_coding 24 | 59710 ensorlt00000012416 sorlg00000029032 vti1b-202 22 1877395 1881006 + mRNA protein_coding 25 | -62972 ensorlt00000012015 sorlg00000009583 oip5-201 22 1750426 1753813 - mRNA protein_coding 26 | -63467 ensorlt00000026770 sorlg00000029808 nusap1-205 22 1753318 1770787 + mRNA protein_coding 27 | -63467 ensorlt00000044577 sorlg00000029808 nusap1-207 22 1753318 1761002 + mRNA protein_coding 28 | -63467 ensorlt00000041261 sorlg00000029808 nusap1-204 22 1753318 1770787 + mRNA protein_coding 29 | -63467 ensorlt00000040692 sorlg00000029808 nusap1-201 22 1753318 1770787 + mRNA protein_coding 30 | -63467 ensorlt00000035455 sorlg00000029808 nusap1-202 22 1753318 1770787 + mRNA protein_coding 31 | -63467 ensorlt00000041023 sorlg00000029808 nusap1-203 22 1753318 1770787 + mRNA protein_coding 32 | -63467 ensorlt00000037984 sorlg00000029808 nusap1-206 22 1753318 1770787 + mRNA protein_coding 33 | 70439 ensorlt00000012465 sorlg00000009933 arg2-201 22 1882456 1888124 - mRNA protein_coding 34 | 75123 ensorlt00000037745 sorlg00000024690 22 1892808 1894478 + mRNA protein_coding 35 | -75537 ensorlt00000012000 sorlg00000009568 chp1-203 22 1741248 1746700 + mRNA protein_coding 36 | -76172 ensorlt00000011998 sorlg00000009568 chp1-201 22 1740613 1746700 + mRNA protein_coding 37 | -76172 ensorlt00000043758 sorlg00000009568 chp1-202 22 1740613 1745064 + mRNA protein_coding 38 | 76231 ensorlt00000012495 sorlg00000009958 rbm25a-201 22 1893916 1900448 + mRNA protein_coding 39 | -82599 ensorlt00000011956 sorlg00000009533 lgmn-201 22 1734186 1740891 + mRNA protein_coding 40 | 84938 ensorlt00000012502 sorlg00000009965 plekhd1-201 22 1902623 1908253 + mRNA protein_coding 41 | 90459 ensorlt00000030404 sorlg00000009965 plekhd1-202 22 1908144 1923959 + mRNA protein_coding 42 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0013_chr16-7720134-7721846.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000030918 sorlg00000026370 16 7721754 7725479 + mRNA protein_coding 3 | -897 ensorlt00000034615 sorlg00000028483 16 7719237 7726170 + mRNA protein_coding 4 | -1396 ensorlt00000035976 sorlg00000029559 16 7718738 7727892 + mRNA protein_coding 5 | -1795 ensorlt00000045648 sorlg00000027038 16 7714608 7718339 - mRNA protein_coding 6 | -6328 ensorlt00000025923 sorlg00000020942 5s_rrna-201 16 7713806 7713924 + rRNA rrna 7 | -9225 ensorlt00000046690 sorlg00000027739 16 7710909 7716160 + mRNA protein_coding 8 | 25191 ensorlt00000028352 sorlg00000003576 cnot10-202 16 7747037 7762281 + mRNA protein_coding 9 | 25191 ensorlt00000032710 sorlg00000003576 cnot10-201 16 7747037 7762281 + mRNA protein_coding 10 | 25202 ensorlt00000004467 sorlg00000003576 cnot10-203 16 7747048 7759356 + mRNA protein_coding 11 | 40528 ensorlt00000028648 sorlg00000003633 ano10a-201 16 7762374 7778680 + mRNA protein_coding 12 | 40528 ensorlt00000032025 sorlg00000003633 ano10a-204 16 7762374 7774851 + mRNA protein_coding 13 | 40528 ensorlt00000027847 sorlg00000003633 ano10a-205 16 7762374 7774851 + mRNA protein_coding 14 | 40528 ensorlt00000041779 sorlg00000003633 ano10a-206 16 7762374 7774851 + mRNA protein_coding 15 | 40528 ensorlt00000004531 sorlg00000003633 ano10a-203 16 7762374 7775269 + mRNA protein_coding 16 | 40528 ensorlt00000035529 sorlg00000003633 ano10a-202 16 7762374 7778680 + mRNA protein_coding 17 | 41609 ensorlt00000004533 sorlg00000003633 ano10a-207 16 7763455 7775269 + mRNA protein_coding 18 | 81669 ensorlt00000004544 sorlg00000003646 snrka-201 16 7781223 7803515 - mRNA protein_coding 19 | 84913 ensorlt00000004565 sorlg00000003663 16 7806759 7819607 + mRNA protein_coding 20 | -90371 ensorlt00000046836 sorlg00000026489 chsy1-201 16 7629763 7636962 + mRNA protein_coding 21 | -94247 ensorlt00000004395 sorlg00000003526 rrp15-201 16 7622321 7625887 - mRNA protein_coding 22 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0014_chr5-19638728-19639909.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -42024 ensorlt00000012721 sorlg00000010143 ptprga-201 5 19596704 19675265 + mRNA protein_coding 3 | 44702 ensorlt00000034060 sorlg00000023114 5 19684611 19686957 + mRNA protein_coding 4 | 66528 ensorlt00000012734 sorlg00000010156 fezf2-201 5 19703415 19706437 - mRNA protein_coding 5 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0015_chr14-24222331-24223586.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2381 ensorlt00000017345 sorlg00000013833 pgap2-201 14 24220856 24225967 - mRNA protein_coding 3 | -19711 ensorlt00000017317 sorlg00000013812 rhogb-201 14 24202620 24215903 + mRNA protein_coding 4 | -26110 ensorlt00000036885 sorlg00000024642 stim1b-201 14 24174573 24196221 - mRNA protein_coding 5 | -26110 ensorlt00000033640 sorlg00000024642 stim1b-202 14 24174573 24196221 - mRNA protein_coding 6 | -29300 ensorlt00000036516 sorlg00000024642 stim1b-203 14 24179480 24193031 - mRNA protein_coding 7 | -57607 ensorlt00000042957 sorlg00000029318 14 24164724 24167600 + mRNA protein_coding 8 | -63372 ensorlt00000034278 sorlg00000024067 14 24157476 24158959 - mRNA protein_coding 9 | -63372 ensorlt00000037346 sorlg00000024067 14 24157464 24158959 - mRNA protein_coding 10 | -68881 ensorlt00000017306 sorlg00000013800 guca1d-201 14 24146858 24153450 - mRNA protein_coding 11 | -82209 ensorlt00000040828 sorlg00000013770 alg8-202 14 24140122 24147172 + mRNA protein_coding 12 | -82230 ensorlt00000030840 sorlg00000013736 ccdc90b-202 14 24132034 24140101 - mRNA protein_coding 13 | -82341 ensorlt00000017269 sorlg00000013770 alg8-201 14 24139990 24147172 + mRNA protein_coding 14 | -82362 ensorlt00000017229 sorlg00000013736 ccdc90b-201 14 24133401 24139969 - mRNA protein_coding 15 | 84021 ensorlt00000028999 sorlg00000028730 14 24306375 24307607 - mRNA protein_coding 16 | 95824 ensorlt00000034040 sorlg00000025574 14 24318277 24319410 - mRNA protein_coding 17 | -99941 ensorlt00000017215 sorlg00000013725 pcf11-202 14 24122390 24132798 + mRNA protein_coding 18 | -99941 ensorlt00000046954 sorlg00000013725 pcf11-201 14 24122390 24132798 + mRNA protein_coding 19 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0016_chr20-15042642-15043458.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 13518 ensorlt00000009283 sorlg00000007404 myrip-201 20 14947205 15056976 - mRNA protein_coding 3 | 18351 ensorlt00000029757 sorlg00000025058 20 15060195 15061809 - mRNA protein_coding 4 | 44462 ensorlt00000009296 sorlg00000007417 ndufb4-201 20 15087920 15091136 + mRNA protein_coding 5 | 46414 ensorlt00000009291 sorlg00000007411 20 15086019 15089872 - mRNA protein_coding 6 | 55117 ensorlt00000038313 sorlg00000007442 hgd-202 20 15086554 15098575 - mRNA protein_coding 7 | 56220 ensorlt00000041276 sorlg00000007442 hgd-201 20 15086554 15099678 - mRNA protein_coding 8 | 57656 ensorlt00000009331 sorlg00000007442 hgd-203 20 15092129 15101114 - mRNA protein_coding 9 | 67864 ensorlt00000035833 sorlg00000007450 arx-201 20 15111322 15119735 + mRNA protein_coding 10 | 67864 ensorlt00000034204 sorlg00000007450 arx-202 20 15111322 15119735 + mRNA protein_coding 11 | 67864 ensorlt00000009338 sorlg00000007450 arx-203 20 15111322 15163442 + mRNA protein_coding 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0017_chr3-309650-310584.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 3012 ensorlt00000032145 sorlg00000023118 3 313596 317617 + mRNA protein_coding 3 | -4683 ensorlt00000041594 sorlg00000023471 3 304967 309552 + mRNA protein_coding 4 | -14278 ensorlt00000043113 sorlg00000022688 vps33b-203 3 278710 295372 - mRNA protein_coding 5 | -14278 ensorlt00000041425 sorlg00000022688 vps33b-201 3 278581 295372 - mRNA protein_coding 6 | -14278 ensorlt00000045274 sorlg00000022688 vps33b-202 3 278581 295372 - mRNA protein_coding 7 | -14947 ensorlt00000032606 sorlg00000026752 hddc3-202 3 294703 299542 + mRNA protein_coding 8 | 16557 ensorlt00000026778 sorlg00000019968 hypk-202 3 327141 328427 + mRNA protein_coding 9 | 16557 ensorlt00000024793 sorlg00000019968 hypk-201 3 327141 332666 + mRNA protein_coding 10 | -26817 ensorlt00000034398 sorlg00000026752 hddc3-201 3 282833 299542 + mRNA protein_coding 11 | 29252 ensorlt00000024798 sorlg00000019973 mfap1-203 3 332840 339836 - mRNA protein_coding 12 | -30961 ensorlt00000026866 sorlg00000028005 3 257879 278689 - mRNA protein_coding 13 | -30961 ensorlt00000029068 sorlg00000028005 3 257902 278689 - mRNA protein_coding 14 | -56446 ensorlt00000031777 sorlg00000027410 3 238909 253204 - mRNA protein_coding 15 | -56446 ensorlt00000044613 sorlg00000027410 3 238909 253204 - mRNA protein_coding 16 | 69963 ensorlt00000034502 sorlg00000019973 mfap1-202 3 332840 380547 - mRNA protein_coding 17 | -81872 ensorlt00000031150 sorlg00000026511 3 227778 231921 + mRNA protein_coding 18 | -94384 ensorlt00000022944 sorlg00000018322 ndufs3-201 3 203393 215266 - mRNA protein_coding 19 | 98129 ensorlt00000043524 sorlg00000019973 mfap1-201 3 332840 408713 - mRNA protein_coding 20 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0018_chr19-1948176-1949405.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -2370 ensorlt00000036726 sorlg00000025662 19 1945806 1949860 + mRNA protein_coding 3 | 26666 ensorlt00000003025 sorlg00000002436 xrcc6-202 19 1976071 1981417 + mRNA protein_coding 4 | 26666 ensorlt00000003027 sorlg00000002436 xrcc6-201 19 1976071 1981819 + mRNA protein_coding 5 | 35921 ensorlt00000033135 sorlg00000029725 josd1-201 19 1985326 1990340 + mRNA protein_coding 6 | -36890 ensorlt00000038704 sorlg00000002421 mrtfab-204 19 1911286 1935809 + mRNA protein_coding 7 | 42900 ensorlt00000032345 sorlg00000026332 cbx7b-203 19 1992305 1997352 + mRNA protein_coding 8 | 42900 ensorlt00000042130 sorlg00000026332 cbx7b-201 19 1992305 1998396 + mRNA protein_coding 9 | 42900 ensorlt00000028264 sorlg00000026332 cbx7b-202 19 1992305 1998396 + mRNA protein_coding 10 | -46522 ensorlt00000003008 sorlg00000002421 mrtfab-203 19 1901654 1931985 + mRNA protein_coding 11 | -55366 ensorlt00000003009 sorlg00000002421 mrtfab-202 19 1892810 1932838 + mRNA protein_coding 12 | -55366 ensorlt00000040426 sorlg00000002421 mrtfab-201 19 1892810 1935809 + mRNA protein_coding 13 | -59867 ensorlt00000002984 sorlg00000002399 vstm4b-201 19 1874725 1888309 - mRNA protein_coding 14 | -78377 ensorlt00000002977 sorlg00000002394 lrrc18b-201 19 1864403 1869799 - mRNA protein_coding 15 | -85119 ensorlt00000002969 sorlg00000002387 si:dkey-191m6.4-201 19 1840851 1863057 - mRNA protein_coding 16 | 87791 ensorlt00000003104 sorlg00000002496 ep300a-201 19 2010342 2037196 - mRNA protein_coding 17 | -88902 ensorlt00000032449 sorlg00000002387 si:dkey-191m6.4-202 19 1840851 1859274 - mRNA protein_coding 18 | -93820 ensorlt00000034221 sorlg00000002387 si:dkey-191m6.4-203 19 1840851 1854356 - mRNA protein_coding 19 | 96736 ensorlt00000040579 sorlg00000002510 l3mbtl2-201 19 2046141 2057879 + mRNA protein_coding 20 | 96736 ensorlt00000003119 sorlg00000002510 l3mbtl2-202 19 2046141 2057879 + mRNA protein_coding 21 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0019_chr14-29614617-29615705.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 8035 ensorlt00000041944 sorlg00000027216 sgcd-201 14 29623740 29750615 + mRNA protein_coding 3 | 11485 ensorlt00000029051 sorlg00000027216 sgcd-202 14 29627190 29748633 + mRNA protein_coding 4 | 27672 ensorlt00000046583 sorlg00000027160 14 29643377 29648245 + mRNA protein_coding 5 | 27672 ensorlt00000046566 sorlg00000027160 14 29643377 29649684 + mRNA protein_coding 6 | 28932 ensorlt00000043620 sorlg00000027160 14 29644637 29649684 + mRNA protein_coding 7 | 28932 ensorlt00000046001 sorlg00000027160 14 29644637 29649684 + mRNA protein_coding 8 | 60071 ensorlt00000045379 sorlg00000027216 sgcd-203 14 29675776 29748633 + mRNA protein_coding 9 | 60071 ensorlt00000036291 sorlg00000027216 sgcd-204 14 29675776 29748633 + mRNA protein_coding 10 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0020_chr22-2405753-2407192.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000027844 sorlg00000028018 tbpl2-202 22 2405923 2412801 + mRNA protein_coding 3 | -944 ensorlt00000013498 sorlg00000028018 tbpl2-201 22 2404809 2407890 + mRNA protein_coding 4 | -3847 ensorlt00000038385 sorlg00000010114 zgc:113944-202 22 2395395 2401906 - mRNA protein_coding 5 | -3847 ensorlt00000034335 sorlg00000010114 zgc:113944-201 22 2394565 2401906 - mRNA protein_coding 6 | -4146 ensorlt00000012683 sorlg00000010114 zgc:113944-203 22 2398540 2401607 - mRNA protein_coding 7 | 5609 ensorlt00000012706 sorlg00000010130 jmjd7-201 22 2404349 2412801 - mRNA protein_coding 8 | 10304 ensorlt00000041852 sorlg00000023986 fbxo34-201 22 2415628 2417496 - mRNA protein_coding 9 | -18091 ensorlt00000040554 sorlg00000025253 22 2385750 2387662 - mRNA protein_coding 10 | 18816 ensorlt00000033430 sorlg00000028430 lgals3b-201 22 2423575 2426008 - mRNA protein_coding 11 | 33054 ensorlt00000012736 sorlg00000010158 22 2434907 2440246 - mRNA protein_coding 12 | -47345 ensorlt00000033843 sorlg00000010109 mapkbp1-204 22 2358408 2383915 + mRNA protein_coding 13 | -48041 ensorlt00000042428 sorlg00000010109 mapkbp1-201 22 2357712 2385971 + mRNA protein_coding 14 | -48041 ensorlt00000029230 sorlg00000010109 mapkbp1-202 22 2357712 2385971 + mRNA protein_coding 15 | -48041 ensorlt00000012677 sorlg00000010109 mapkbp1-203 22 2357712 2383915 + mRNA protein_coding 16 | 53751 ensorlt00000034426 sorlg00000023322 22 2441301 2460943 - mRNA protein_coding 17 | 56037 ensorlt00000035935 sorlg00000023322 22 2442189 2463229 - mRNA protein_coding 18 | 58521 ensorlt00000045918 sorlg00000021949 22 2465713 2469483 + mRNA protein_coding 19 | 65257 ensorlt00000031016 sorlg00000027454 22 2472449 2477940 + mRNA protein_coding 20 | 67086 ensorlt00000027634 sorlg00000023316 22 2474278 2474362 + snoRNA snorna 21 | -67135 ensorlt00000044746 sorlg00000022155 22 2338618 2345348 + mRNA protein_coding 22 | 69761 ensorlt00000034617 sorlg00000026312 22 2476953 2477037 + snoRNA snorna 23 | 73639 ensorlt00000012850 sorlg00000010245 22 2480831 2485332 + mRNA protein_coding 24 | 82582 ensorlt00000012893 sorlg00000010288 psma3-201 22 2483540 2489774 - mRNA protein_coding 25 | 88381 ensorlt00000012932 sorlg00000010318 snx6-201 22 2490424 2495573 - mRNA protein_coding 26 | -90268 ensorlt00000012628 sorlg00000010072 22 2315485 2319110 + mRNA protein_coding 27 | 91947 ensorlt00000012944 sorlg00000010332 cfl2-202 22 2497903 2499139 - mRNA protein_coding 28 | 94354 ensorlt00000040763 sorlg00000010332 cfl2-201 22 2497903 2501546 - mRNA protein_coding 29 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0021_chr16-7663486-7664331.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -33723 ensorlt00000046836 sorlg00000026489 chsy1-201 16 7629763 7636962 + mRNA protein_coding 3 | -37599 ensorlt00000004395 sorlg00000003526 rrp15-201 16 7622321 7625887 - mRNA protein_coding 4 | 46578 ensorlt00000046690 sorlg00000027739 16 7710909 7716160 + mRNA protein_coding 5 | 49475 ensorlt00000025923 sorlg00000020942 5s_rrna-201 16 7713806 7713924 + rRNA rrna 6 | 54008 ensorlt00000045648 sorlg00000027038 16 7714608 7718339 - mRNA protein_coding 7 | 54407 ensorlt00000035976 sorlg00000029559 16 7718738 7727892 + mRNA protein_coding 8 | 54906 ensorlt00000034615 sorlg00000028483 16 7719237 7726170 + mRNA protein_coding 9 | -57256 ensorlt00000004389 sorlg00000003521 tcaim-201 16 7606230 7623541 + mRNA protein_coding 10 | 57423 ensorlt00000030918 sorlg00000026370 16 7721754 7725479 + mRNA protein_coding 11 | -57904 ensorlt00000030716 sorlg00000028231 ggctb-201 16 7599040 7605582 - mRNA protein_coding 12 | 82706 ensorlt00000032710 sorlg00000003576 cnot10-201 16 7747037 7762281 + mRNA protein_coding 13 | 82706 ensorlt00000028352 sorlg00000003576 cnot10-202 16 7747037 7762281 + mRNA protein_coding 14 | 82717 ensorlt00000004467 sorlg00000003576 cnot10-203 16 7747048 7759356 + mRNA protein_coding 15 | -86122 ensorlt00000004350 sorlg00000003493 slc6a20-201 16 7551242 7577364 - mRNA protein_coding 16 | 98043 ensorlt00000032025 sorlg00000003633 ano10a-204 16 7762374 7774851 + mRNA protein_coding 17 | 98043 ensorlt00000027847 sorlg00000003633 ano10a-205 16 7762374 7774851 + mRNA protein_coding 18 | 98043 ensorlt00000041779 sorlg00000003633 ano10a-206 16 7762374 7774851 + mRNA protein_coding 19 | 98043 ensorlt00000004531 sorlg00000003633 ano10a-203 16 7762374 7775269 + mRNA protein_coding 20 | 98043 ensorlt00000028648 sorlg00000003633 ano10a-201 16 7762374 7778680 + mRNA protein_coding 21 | 98043 ensorlt00000035529 sorlg00000003633 ano10a-202 16 7762374 7778680 + mRNA protein_coding 22 | 99124 ensorlt00000004533 sorlg00000003633 ano10a-207 16 7763455 7775269 + mRNA protein_coding 23 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0022_chr9-1939074-1940052.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 725 ensorlt00000000515 sorlg00000000417 9 1935527 1940777 - mRNA protein_coding 3 | 6304 ensorlt00000045125 sorlg00000024554 9 1943765 1946356 - mRNA protein_coding 4 | 8427 ensorlt00000035817 sorlg00000024525 9 1948479 1951063 + mRNA protein_coding 5 | -15146 ensorlt00000000492 sorlg00000000401 siat8c2-201 9 1923928 1930131 + mRNA protein_coding 6 | 18800 ensorlt00000000568 sorlg00000000460 zgc:172315-201 9 1951151 1958852 - mRNA protein_coding 7 | -20012 ensorlt00000000472 sorlg00000000384 9 1919062 1922638 + mRNA protein_coding 8 | 24786 ensorlt00000000572 sorlg00000000466 tal2-201 9 1964500 1964838 - mRNA protein_coding 9 | 44482 ensorlt00000031314 sorlg00000030010 9 1967230 1984534 - mRNA protein_coding 10 | -50784 ensorlt00000000458 sorlg00000000372 zenzai-202 9 1878531 1888290 - mRNA protein_coding 11 | -51051 ensorlt00000035514 sorlg00000000372 zenzai-201 9 1875739 1888023 - mRNA protein_coding 12 | 55117 ensorlt00000000597 sorlg00000000488 krt1-c5-202 9 1988611 1995169 - mRNA protein_coding 13 | 55649 ensorlt00000000595 sorlg00000000488 krt1-c5-201 9 1988298 1995701 - mRNA protein_coding 14 | 71396 ensorlt00000000611 sorlg00000000498 si:ch211-236k19.2-201 9 2004120 2011448 - mRNA protein_coding 15 | -85099 ensorlt00000039311 sorlg00000000353 9 1853975 1866218 + mRNA protein_coding 16 | 86445 ensorlt00000000625 sorlg00000000509 ptgs1-201 9 2026497 2038137 + mRNA protein_coding 17 | -87386 ensorlt00000036394 sorlg00000000353 9 1851688 1866218 + mRNA protein_coding 18 | -87386 ensorlt00000000429 sorlg00000000353 9 1851688 1866218 + mRNA protein_coding 19 | -90146 ensorlt00000000419 sorlg00000000346 9 1847206 1848928 - mRNA protein_coding 20 | -94825 ensorlt00000032405 sorlg00000027430 9 1840506 1844249 - mRNA protein_coding 21 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0024_chr2-22706556-22707650.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 5505 ensorlt00000007125 sorlg00000005666 cdadc1-201 2 22704787 22713155 - mRNA protein_coding 3 | -6146 ensorlt00000007111 sorlg00000005654 cab39l-201 2 22700410 22707641 + mRNA protein_coding 4 | 14565 ensorlt00000007132 sorlg00000005672 rcbtb1-202 2 22713176 22722215 - mRNA protein_coding 5 | 14887 ensorlt00000029038 sorlg00000005672 rcbtb1-201 2 22710815 22722537 - mRNA protein_coding 6 | 21243 ensorlt00000036205 sorlg00000025753 2 22728893 22795999 + mRNA protein_coding 7 | 48803 ensorlt00000039537 sorlg00000025753 2 22756453 22795999 + mRNA protein_coding 8 | -57971 ensorlt00000030202 sorlg00000005630 mcf2la-208 2 22648585 22692691 + mRNA protein_coding 9 | -65993 ensorlt00000035986 sorlg00000005630 mcf2la-206 2 22640563 22692691 + mRNA protein_coding 10 | -65993 ensorlt00000007094 sorlg00000005630 mcf2la-207 2 22640563 22691714 + mRNA protein_coding 11 | -66205 ensorlt00000028018 sorlg00000005481 2 22610888 22640351 - mRNA protein_coding 12 | -66538 ensorlt00000007089 sorlg00000005630 mcf2la-205 2 22640018 22691714 + mRNA protein_coding 13 | -69873 ensorlt00000030116 sorlg00000005630 mcf2la-204 2 22636683 22692691 + mRNA protein_coding 14 | -76132 ensorlt00000041729 sorlg00000005630 mcf2la-203 2 22630424 22692691 + mRNA protein_coding 15 | -76256 ensorlt00000027023 sorlg00000005630 mcf2la-201 2 22630300 22692039 + mRNA protein_coding 16 | -76256 ensorlt00000028403 sorlg00000005630 mcf2la-202 2 22630300 22691714 + mRNA protein_coding 17 | -78348 ensorlt00000006905 sorlg00000005481 2 22610888 22628208 - mRNA protein_coding 18 | -86009 ensorlt00000036225 sorlg00000005481 2 22610888 22620547 - mRNA protein_coding 19 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0025_chr2-23324373-23325538.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -1866 ensorlt00000007888 sorlg00000006275 gart-201 2 23313034 23322507 - mRNA protein_coding 3 | -31849 ensorlt00000032912 sorlg00000028237 2 23291361 23292524 - mRNA protein_coding 4 | -34183 ensorlt00000007813 sorlg00000006216 2 23286187 23290190 - mRNA protein_coding 5 | -41154 ensorlt00000007807 sorlg00000006210 2 23270364 23283219 - mRNA protein_coding 6 | -64040 ensorlt00000007796 sorlg00000024129 2 23260333 23267964 + mRNA protein_coding 7 | -66689 ensorlt00000036795 sorlg00000024129 2 23257684 23271878 + mRNA protein_coding 8 | -73023 ensorlt00000031726 sorlg00000006194 2 23251350 23259135 + mRNA protein_coding 9 | -73023 ensorlt00000033433 sorlg00000006194 2 23251350 23256310 + mRNA protein_coding 10 | -73023 ensorlt00000043729 sorlg00000006194 2 23251350 23256310 + mRNA protein_coding 11 | -73023 ensorlt00000035108 sorlg00000006194 2 23251350 23256310 + mRNA protein_coding 12 | -73023 ensorlt00000043890 sorlg00000006194 2 23251350 23256310 + mRNA protein_coding 13 | -73023 ensorlt00000007789 sorlg00000006194 2 23251350 23256310 + mRNA protein_coding 14 | -73393 ensorlt00000031087 sorlg00000006194 2 23250980 23256310 + mRNA protein_coding 15 | -76319 ensorlt00000044153 sorlg00000006194 2 23248054 23258916 + mRNA protein_coding 16 | -76490 ensorlt00000033097 sorlg00000006194 2 23247883 23256310 + mRNA protein_coding 17 | -77995 ensorlt00000031706 sorlg00000006194 2 23246378 23256310 + mRNA protein_coding 18 | -84350 ensorlt00000011113 sorlg00000006182 2 23240023 23248234 + mRNA protein_coding 19 | -84576 ensorlt00000007778 sorlg00000006182 2 23239797 23247184 + mRNA protein_coding 20 | -87708 ensorlt00000035200 sorlg00000025289 2 23234134 23236665 - mRNA protein_coding 21 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0026_chr12-2187537-2190115.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -10253 ensorlt00000001441 sorlg00000001168 12 2177284 2190978 + mRNA protein_coding 3 | 49416 ensorlt00000001474 sorlg00000001195 sez6l-201 12 2239531 2260854 + mRNA protein_coding 4 | 49416 ensorlt00000001475 sorlg00000001195 sez6l-202 12 2239531 2260854 + mRNA protein_coding 5 | -69907 ensorlt00000037848 sorlg00000001133 grk3-203 12 2117630 2161490 + mRNA protein_coding 6 | -69907 ensorlt00000035830 sorlg00000001133 grk3-202 12 2117630 2161615 + mRNA protein_coding 7 | -69907 ensorlt00000001400 sorlg00000001133 grk3-201 12 2117630 2163782 + mRNA protein_coding 8 | -74547 ensorlt00000040453 sorlg00000022438 cryba4-202 12 2112990 2117609 + mRNA protein_coding 9 | 76626 ensorlt00000001484 sorlg00000001204 12 2266741 2269204 + mRNA protein_coding 10 | 77082 ensorlt00000015052 sorlg00000012019 12 2267197 2268484 + mRNA protein_coding 11 | -77568 ensorlt00000010235 sorlg00000022438 cryba4-201 12 2109969 2113945 + mRNA protein_coding 12 | 79940 ensorlt00000040024 sorlg00000027874 12 2270055 2276841 + mRNA protein_coding 13 | -83251 ensorlt00000001367 sorlg00000001108 crybb1-201 12 2101159 2104286 - mRNA protein_coding 14 | -86816 ensorlt00000001355 sorlg00000001095 acads-201 12 2092223 2100721 - mRNA protein_coding 15 | 87170 ensorlt00000038851 sorlg00000001244 si:ch211-48m9.1-202 12 2273376 2277285 - mRNA protein_coding 16 | -94734 ensorlt00000001337 sorlg00000001086 cldn5b-201 12 2092803 2093450 + mRNA protein_coding 17 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0027_chr5-30060867-30062266.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -778 ensorlt00000034046 sorlg00000024114 5 30056742 30060089 - mRNA protein_coding 3 | 26639 ensorlt00000041674 sorlg00000022054 5 30088905 30092924 + mRNA protein_coding 4 | 33172 ensorlt00000035208 sorlg00000016608 dlgap4b-201 5 30095438 30137126 + mRNA protein_coding 5 | 33172 ensorlt00000020790 sorlg00000016608 dlgap4b-202 5 30095438 30137126 + mRNA protein_coding 6 | 75056 ensorlt00000042192 sorlg00000022604 5 30137322 30142374 + mRNA protein_coding 7 | 87724 ensorlt00000020801 sorlg00000016619 myl9a-202 5 30144761 30149990 - mRNA protein_coding 8 | 88817 ensorlt00000039756 sorlg00000016619 myl9a-201 5 30144761 30151083 - mRNA protein_coding 9 | 89452 ensorlt00000020834 sorlg00000016643 zgc:123305-201 5 30151718 30168877 + mRNA protein_coding 10 | 92246 ensorlt00000040822 sorlg00000016643 zgc:123305-202 5 30154512 30168877 + mRNA protein_coding 11 | 92246 ensorlt00000044544 sorlg00000016643 zgc:123305-203 5 30154512 30168877 + mRNA protein_coding 12 | 92246 ensorlt00000033264 sorlg00000016643 zgc:123305-204 5 30154512 30168877 + mRNA protein_coding 13 | -94335 ensorlt00000028805 sorlg00000024972 5 29966532 29969294 + mRNA protein_coding 14 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0028_chr6-1003683-1004493.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 53144 ensorlt00000023961 sorlg00000019230 ptprz1a-201 6 999004 1057637 - mRNA protein_coding 3 | -83141 ensorlt00000032648 sorlg00000030143 ano1-201 6 920542 990879 + mRNA protein_coding 4 | -95299 ensorlt00000028612 sorlg00000026455 6 897005 908384 - mRNA protein_coding 5 | -95299 ensorlt00000034185 sorlg00000026455 6 901158 908384 - mRNA protein_coding 6 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0030_chr14-29286331-29287419.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -6650 ensorlt00000019460 sorlg00000015542 galnt10-201 14 29234584 29279681 - mRNA protein_coding 3 | 13529 ensorlt00000042885 sorlg00000029231 14 29298395 29300948 - mRNA protein_coding 4 | 23652 ensorlt00000034962 sorlg00000024921 14 29307506 29311071 - mRNA protein_coding 5 | -59399 ensorlt00000043680 sorlg00000023108 14 29226932 29228455 + mRNA protein_coding 6 | 64260 ensorlt00000040008 sorlg00000023427 mfap3-201 14 29349354 29351679 - mRNA protein_coding 7 | 86842 ensorlt00000019481 sorlg00000015559 fam114a2-201 14 29374261 29380591 + mRNA protein_coding 8 | 93360 ensorlt00000019507 sorlg00000015579 cnot8-201 14 29380779 29386648 + mRNA protein_coding 9 | 94486 ensorlt00000042567 sorlg00000015579 cnot8-202 14 29381905 29386648 + mRNA protein_coding 10 | -95222 ensorlt00000031533 sorlg00000029112 14 29189826 29191109 - mRNA protein_coding 11 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0031_chr7-26640756-26641574.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 74898 ensorlt00000028663 sorlg00000028539 7 26712747 26716472 - mRNA protein_coding 3 | -80713 ensorlt00000027919 sorlg00000024721 7 26560043 26563929 + mRNA protein_coding 4 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0032_chr6-4948049-4949056.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000043528 sorlg00000025444 6 4945100 4948063 - mRNA protein_coding 3 | 16631 ensorlt00000023204 sorlg00000018559 zgc:158868-201 6 4950567 4965687 - mRNA protein_coding 4 | -30407 ensorlt00000023237 sorlg00000018585 bcar1-203 6 4917642 4942617 + mRNA protein_coding 5 | -44456 ensorlt00000040494 sorlg00000018585 bcar1-202 6 4903593 4942617 + mRNA protein_coding 6 | -66859 ensorlt00000044728 sorlg00000018585 bcar1-201 6 4881190 4942915 + mRNA protein_coding 7 | 73146 ensorlt00000023197 sorlg00000018545 lrp5-203 6 4974192 5022202 - mRNA protein_coding 8 | 75635 ensorlt00000046346 sorlg00000018545 lrp5-201 6 4971674 5024691 - mRNA protein_coding 9 | 75635 ensorlt00000036180 sorlg00000018545 lrp5-202 6 4971674 5024691 - mRNA protein_coding 10 | -79987 ensorlt00000042084 sorlg00000018612 6 4868062 4877914 + mRNA protein_coding 11 | -79987 ensorlt00000023269 sorlg00000018612 6 4868062 4877914 + mRNA protein_coding 12 | -96796 ensorlt00000023300 sorlg00000018643 galn-201 6 4842078 4851253 - mRNA protein_coding 13 | -97102 ensorlt00000023305 sorlg00000018643 galn-202 6 4842078 4850947 - mRNA protein_coding 14 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0033_chr9-1940281-1941248.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000000515 sorlg00000000417 9 1935527 1940777 - mRNA protein_coding 3 | 5108 ensorlt00000045125 sorlg00000024554 9 1943765 1946356 - mRNA protein_coding 4 | 7231 ensorlt00000035817 sorlg00000024525 9 1948479 1951063 + mRNA protein_coding 5 | -16353 ensorlt00000000492 sorlg00000000401 siat8c2-201 9 1923928 1930131 + mRNA protein_coding 6 | 17604 ensorlt00000000568 sorlg00000000460 zgc:172315-201 9 1951151 1958852 - mRNA protein_coding 7 | -21219 ensorlt00000000472 sorlg00000000384 9 1919062 1922638 + mRNA protein_coding 8 | 23590 ensorlt00000000572 sorlg00000000466 tal2-201 9 1964500 1964838 - mRNA protein_coding 9 | 43286 ensorlt00000031314 sorlg00000030010 9 1967230 1984534 - mRNA protein_coding 10 | -51991 ensorlt00000000458 sorlg00000000372 zenzai-202 9 1878531 1888290 - mRNA protein_coding 11 | -52258 ensorlt00000035514 sorlg00000000372 zenzai-201 9 1875739 1888023 - mRNA protein_coding 12 | 53921 ensorlt00000000597 sorlg00000000488 krt1-c5-202 9 1988611 1995169 - mRNA protein_coding 13 | 54453 ensorlt00000000595 sorlg00000000488 krt1-c5-201 9 1988298 1995701 - mRNA protein_coding 14 | 70200 ensorlt00000000611 sorlg00000000498 si:ch211-236k19.2-201 9 2004120 2011448 - mRNA protein_coding 15 | 85249 ensorlt00000000625 sorlg00000000509 ptgs1-201 9 2026497 2038137 + mRNA protein_coding 16 | -86306 ensorlt00000039311 sorlg00000000353 9 1853975 1866218 + mRNA protein_coding 17 | -88593 ensorlt00000000429 sorlg00000000353 9 1851688 1866218 + mRNA protein_coding 18 | -88593 ensorlt00000036394 sorlg00000000353 9 1851688 1866218 + mRNA protein_coding 19 | -91353 ensorlt00000000419 sorlg00000000346 9 1847206 1848928 - mRNA protein_coding 20 | -96032 ensorlt00000032405 sorlg00000027430 9 1840506 1844249 - mRNA protein_coding 21 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0034_chr14-19955750-19956691.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 14624 ensorlt00000031151 sorlg00000029603 rps6ka4-202 14 19957802 19971315 - mRNA protein_coding 3 | 17116 ensorlt00000044933 sorlg00000029603 rps6ka4-201 14 19957802 19973807 - mRNA protein_coding 4 | 17134 ensorlt00000031900 sorlg00000029603 rps6ka4-203 14 19962524 19973825 - mRNA protein_coding 5 | 30221 ensorlt00000013613 sorlg00000010852 stip1-202 14 19978576 19986912 - mRNA protein_coding 6 | 33115 ensorlt00000013614 sorlg00000010852 stip1-201 14 19978513 19989806 - mRNA protein_coding 7 | 33997 ensorlt00000038874 sorlg00000025822 spata22-201 14 19990688 19998823 + mRNA protein_coding 8 | 33997 ensorlt00000043058 sorlg00000025822 spata22-202 14 19990688 19998823 + mRNA protein_coding 9 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0035_chr6-2209392-2211073.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 916 ensorlt00000028066 sorlg00000024800 6 2208558 2211989 - mRNA protein_coding 3 | -11983 ensorlt00000024773 sorlg00000019951 lrrk2-201 6 2138866 2197409 - mRNA protein_coding 4 | 33517 ensorlt00000045881 sorlg00000022008 6 2244590 2247357 + mRNA protein_coding 5 | 60664 ensorlt00000024762 sorlg00000019937 zgc:103499-201 6 2271737 2273890 + mRNA protein_coding 6 | -92796 ensorlt00000024821 sorlg00000019988 slc6a15-201 6 2116596 2136596 + mRNA protein_coding 7 | 94755 ensorlt00000027967 sorlg00000028369 6 2304565 2305828 - mRNA protein_coding 8 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0036_chr1-1608911-1609767.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -4370 ensorlt00000000072 sorlg00000000055 1 1576629 1604541 - mRNA protein_coding 3 | 5523 ensorlt00000040497 sorlg00000000062 arhgap19-201 1 1606039 1615290 - mRNA protein_coding 4 | 5523 ensorlt00000032161 sorlg00000000062 arhgap19-202 1 1606039 1615290 - mRNA protein_coding 5 | 5523 ensorlt00000000074 sorlg00000000062 arhgap19-203 1 1606039 1615290 - mRNA protein_coding 6 | 10626 ensorlt00000000075 sorlg00000000064 si:ch211-133l11.10-202 1 1618265 1620393 - mRNA protein_coding 7 | 10634 ensorlt00000047053 sorlg00000000064 si:ch211-133l11.10-201 1 1618265 1620401 - mRNA protein_coding 8 | 22871 ensorlt00000047064 sorlg00000027625 dla-201 1 1632638 1640828 + mRNA protein_coding 9 | -50087 ensorlt00000032515 sorlg00000027690 1 1555542 1558824 - mRNA protein_coding 10 | 51729 ensorlt00000044437 sorlg00000026423 1 1642274 1661496 - mRNA protein_coding 11 | 52041 ensorlt00000046946 sorlg00000026423 1 1647230 1661808 - mRNA protein_coding 12 | 75827 ensorlt00000000086 sorlg00000000069 hk1-201 1 1661829 1685594 - mRNA protein_coding 13 | 81381 ensorlt00000000089 sorlg00000000075 myom2a-201 1 1691148 1720250 + mRNA protein_coding 14 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0037_chr11-14611139-14611909.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 912 ensorlt00000007402 sorlg00000005883 si:ch73-160i9.1-201 11 14601378 14612821 - mRNA protein_coding 3 | -5514 ensorlt00000043573 sorlg00000005883 si:ch73-160i9.1-202 11 14601378 14605625 - mRNA protein_coding 4 | 17282 ensorlt00000040699 sorlg00000029494 11 14629191 14639498 + mRNA protein_coding 5 | -21544 ensorlt00000007375 sorlg00000005862 slc39a7-201 11 14589595 14597033 + mRNA protein_coding 6 | 23171 ensorlt00000037812 sorlg00000029494 11 14635080 14639498 + mRNA protein_coding 7 | 29930 ensorlt00000007420 sorlg00000005901 si:ch211-171h4.3-201 11 14641839 14647014 + mRNA protein_coding 8 | -53304 ensorlt00000007352 sorlg00000005843 mfsd2ab-201 11 14557835 14570612 + mRNA protein_coding 9 | 58761 ensorlt00000007466 sorlg00000005937 necap1-202 11 14659820 14670670 - mRNA protein_coding 10 | 59814 ensorlt00000007463 sorlg00000005937 necap1-201 11 14659820 14671723 - mRNA protein_coding 11 | 59987 ensorlt00000039400 sorlg00000022106 zgc:194578-201 11 14671896 14682483 + mRNA protein_coding 12 | 60650 ensorlt00000037831 sorlg00000022106 zgc:194578-204 11 14672559 14682483 + mRNA protein_coding 13 | 60650 ensorlt00000031760 sorlg00000022106 zgc:194578-205 11 14672559 14682483 + mRNA protein_coding 14 | 60650 ensorlt00000042327 sorlg00000022106 zgc:194578-203 11 14672559 14689140 + mRNA protein_coding 15 | 60650 ensorlt00000040473 sorlg00000022106 zgc:194578-202 11 14672559 14699173 + mRNA protein_coding 16 | 77036 ensorlt00000007480 sorlg00000005946 si:ch211-232m10.6-201 11 14688945 14693859 + mRNA protein_coding 17 | 89824 ensorlt00000007496 sorlg00000005957 rcvrn3-201 11 14697355 14701733 - mRNA protein_coding 18 | -96715 ensorlt00000036868 sorlg00000024045 myclb-201 11 14505595 14514424 - mRNA protein_coding 19 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0038_chr18-19963184-19964018.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 35228 ensorlt00000033449 sorlg00000026347 si:ch211-200p22.4-203 18 19999246 20147782 + mRNA protein_coding 3 | 35228 ensorlt00000030927 sorlg00000026347 si:ch211-200p22.4-204 18 19999246 20147782 + mRNA protein_coding 4 | 35228 ensorlt00000043377 sorlg00000026347 si:ch211-200p22.4-201 18 19999246 20148051 + mRNA protein_coding 5 | 35228 ensorlt00000031475 sorlg00000026347 si:ch211-200p22.4-202 18 19999246 20148051 + mRNA protein_coding 6 | 36363 ensorlt00000037062 sorlg00000026347 si:ch211-200p22.4-205 18 20000381 20148199 + mRNA protein_coding 7 | 36418 ensorlt00000029637 sorlg00000026347 si:ch211-200p22.4-207 18 20000436 20147782 + mRNA protein_coding 8 | 36418 ensorlt00000041205 sorlg00000026347 si:ch211-200p22.4-208 18 20000436 20147782 + mRNA protein_coding 9 | 36418 ensorlt00000044735 sorlg00000026347 si:ch211-200p22.4-206 18 20000436 20148051 + mRNA protein_coding 10 | -60959 ensorlt00000044959 sorlg00000024840 zgc:162171-201 18 19902225 19967554 + mRNA protein_coding 11 | -90874 ensorlt00000010480 sorlg00000008345 18 19844477 19872310 - mRNA protein_coding 12 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0039_chr24-10286328-10287069.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 0 ensorlt00000030196 sorlg00000022999 mfsd4b-201 24 10278218 10286742 - mRNA protein_coding 3 | 0 ensorlt00000040621 sorlg00000022999 mfsd4b-202 24 10279539 10286742 - mRNA protein_coding 4 | 14121 ensorlt00000019005 sorlg00000015165 mfsd4b-201 24 10292654 10301190 - mRNA protein_coding 5 | -45692 ensorlt00000018996 sorlg00000015155 rev3l-201 24 10240636 10279322 + mRNA protein_coding 6 | 47189 ensorlt00000019009 sorlg00000015171 slc16a10-201 24 10298686 10334258 - mRNA protein_coding 7 | -50492 ensorlt00000018956 sorlg00000015125 24 10235836 10243073 + mRNA protein_coding 8 | 54585 ensorlt00000019024 sorlg00000015183 rpf2-201 24 10336286 10341654 - mRNA protein_coding 9 | -57108 ensorlt00000042752 sorlg00000028764 24 10229220 10232247 + mRNA protein_coding 10 | -58591 ensorlt00000041477 sorlg00000030604 24 10221782 10227737 - mRNA protein_coding 11 | -59914 ensorlt00000046904 sorlg00000030604 24 10219908 10226414 - mRNA protein_coding 12 | 65374 ensorlt00000019051 sorlg00000015204 amd1-201 24 10344291 10352443 - mRNA protein_coding 13 | 65829 ensorlt00000044271 sorlg00000015247 cdk19-202 24 10352898 10355576 + mRNA protein_coding 14 | 65829 ensorlt00000019103 sorlg00000015247 cdk19-201 24 10352898 10383633 + mRNA protein_coding 15 | 66294 ensorlt00000019101 sorlg00000015247 cdk19-203 24 10353363 10383633 + mRNA protein_coding 16 | -78853 ensorlt00000018947 sorlg00000015119 naa30-201 24 10207475 10215451 + mRNA protein_coding 17 | -94225 ensorlt00000018940 sorlg00000015112 24 10192103 10204020 + mRNA protein_coding 18 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0040_chr1-28861433-28862812.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 3270 ensorlt00000015172 sorlg00000012122 gnav1-201 1 28837663 28866082 - mRNA protein_coding 3 | 10962 ensorlt00000015203 sorlg00000012151 pcyt2-202 1 28868106 28873774 - mRNA protein_coding 4 | 10962 ensorlt00000009918 sorlg00000012151 pcyt2-201 1 28868106 28873774 - mRNA protein_coding 5 | 16963 ensorlt00000015219 sorlg00000012165 sirt7-201 1 28876317 28879775 - mRNA protein_coding 6 | -28171 ensorlt00000030591 sorlg00000028541 1 28833262 28837005 + mRNA protein_coding 7 | 30048 ensorlt00000035128 sorlg00000027084 1 28879796 28892860 - mRNA protein_coding 8 | -30816 ensorlt00000015141 sorlg00000012098 npb-201 1 28830617 28831202 + mRNA protein_coding 9 | -36016 ensorlt00000015132 sorlg00000012088 sgsh-201 1 28825417 28830167 + mRNA protein_coding 10 | -36421 ensorlt00000046125 sorlg00000026002 1 28818237 28825012 - mRNA protein_coding 11 | -38044 ensorlt00000036620 sorlg00000028837 1 28823389 28825844 + mRNA protein_coding 12 | 38094 ensorlt00000015228 sorlg00000012170 mafg-201 1 28900118 28900906 - mRNA protein_coding 13 | -39576 ensorlt00000030211 sorlg00000012068 slc26a11-201 1 28812949 28821857 - mRNA protein_coding 14 | -41736 ensorlt00000015110 sorlg00000012068 slc26a11-202 1 28812949 28819697 - mRNA protein_coding 15 | -50999 ensorlt00000015073 sorlg00000012039 1 28809939 28810434 - mRNA protein_coding 16 | -53485 ensorlt00000015064 sorlg00000012029 1 28797353 28807948 - mRNA protein_coding 17 | -57807 ensorlt00000030345 sorlg00000022735 1 28803626 28804432 + mRNA protein_coding 18 | 74221 ensorlt00000038723 sorlg00000027940 1 28927014 28937033 - mRNA protein_coding 19 | 84379 ensorlt00000031592 sorlg00000012206 myadml2-202 1 28943708 28947191 - mRNA protein_coding 20 | 84379 ensorlt00000015280 sorlg00000012206 myadml2-201 1 28943708 28947191 - mRNA protein_coding 21 | -89844 ensorlt00000015046 sorlg00000012018 nanos3-201 1 28770845 28771589 - mRNA protein_coding 22 | 99890 ensorlt00000015311 sorlg00000012233 aspscr1-201 1 28952060 28962702 - mRNA protein_coding 23 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0041_chr1-28858118-28859215.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 6867 ensorlt00000015172 sorlg00000012122 gnav1-201 1 28837663 28866082 - mRNA protein_coding 3 | 14559 ensorlt00000015203 sorlg00000012151 pcyt2-202 1 28868106 28873774 - mRNA protein_coding 4 | 14559 ensorlt00000009918 sorlg00000012151 pcyt2-201 1 28868106 28873774 - mRNA protein_coding 5 | 20560 ensorlt00000015219 sorlg00000012165 sirt7-201 1 28876317 28879775 - mRNA protein_coding 6 | -24856 ensorlt00000030591 sorlg00000028541 1 28833262 28837005 + mRNA protein_coding 7 | -27501 ensorlt00000015141 sorlg00000012098 npb-201 1 28830617 28831202 + mRNA protein_coding 8 | -32701 ensorlt00000015132 sorlg00000012088 sgsh-201 1 28825417 28830167 + mRNA protein_coding 9 | -33106 ensorlt00000046125 sorlg00000026002 1 28818237 28825012 - mRNA protein_coding 10 | 33645 ensorlt00000035128 sorlg00000027084 1 28879796 28892860 - mRNA protein_coding 11 | -34729 ensorlt00000036620 sorlg00000028837 1 28823389 28825844 + mRNA protein_coding 12 | -36261 ensorlt00000030211 sorlg00000012068 slc26a11-201 1 28812949 28821857 - mRNA protein_coding 13 | -38421 ensorlt00000015110 sorlg00000012068 slc26a11-202 1 28812949 28819697 - mRNA protein_coding 14 | 41691 ensorlt00000015228 sorlg00000012170 mafg-201 1 28900118 28900906 - mRNA protein_coding 15 | -47684 ensorlt00000015073 sorlg00000012039 1 28809939 28810434 - mRNA protein_coding 16 | -50170 ensorlt00000015064 sorlg00000012029 1 28797353 28807948 - mRNA protein_coding 17 | -54492 ensorlt00000030345 sorlg00000022735 1 28803626 28804432 + mRNA protein_coding 18 | 77818 ensorlt00000038723 sorlg00000027940 1 28927014 28937033 - mRNA protein_coding 19 | -86529 ensorlt00000015046 sorlg00000012018 nanos3-201 1 28770845 28771589 - mRNA protein_coding 20 | 87976 ensorlt00000015280 sorlg00000012206 myadml2-201 1 28943708 28947191 - mRNA protein_coding 21 | 87976 ensorlt00000031592 sorlg00000012206 myadml2-202 1 28943708 28947191 - mRNA protein_coding 22 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0042_chr3-16474087-16474976.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -3223 ensorlt00000005943 sorlg00000004724 grk1-201 3 16470864 16479209 + mRNA protein_coding 3 | 5613 ensorlt00000005964 sorlg00000004739 3 16480589 16494851 + mRNA protein_coding 4 | -12344 ensorlt00000005931 sorlg00000004713 tmco3-201 3 16461743 16468008 + mRNA protein_coding 5 | -15707 ensorlt00000005914 sorlg00000004697 dcun1d2b-201 3 16457075 16458380 - mRNA protein_coding 6 | -19580 ensorlt00000005910 sorlg00000004693 adprhl1-201 3 16446196 16454507 - mRNA protein_coding 7 | -28166 ensorlt00000005882 sorlg00000004671 grtp1-201 3 16439229 16445921 - mRNA protein_coding 8 | 29106 ensorlt00000027718 sorlg00000004757 gas6-202 3 16481317 16504082 - mRNA protein_coding 9 | 29106 ensorlt00000005988 sorlg00000004757 gas6-201 3 16476723 16504082 - mRNA protein_coding 10 | 39643 ensorlt00000006078 sorlg00000004826 pros1-201 3 16505885 16514619 - mRNA protein_coding 11 | -42368 ensorlt00000005855 sorlg00000004652 lamp1a-201 3 16431719 16438998 + mRNA protein_coding 12 | -48961 ensorlt00000005816 sorlg00000004625 cul4a-201 3 16425126 16429916 + mRNA protein_coding 13 | -52098 ensorlt00000005776 sorlg00000004590 tgfbrap1-202 3 16410712 16421989 - mRNA protein_coding 14 | -52098 ensorlt00000027809 sorlg00000004590 tgfbrap1-201 3 16410712 16421989 - mRNA protein_coding 15 | -53982 ensorlt00000005774 sorlg00000004590 tgfbrap1-203 3 16412068 16420105 - mRNA protein_coding 16 | -66476 ensorlt00000035281 sorlg00000004577 3 16392170 16407611 - mRNA protein_coding 17 | -66476 ensorlt00000005757 sorlg00000004577 3 16392170 16407611 - mRNA protein_coding 18 | -82388 ensorlt00000005744 sorlg00000004567 lims1-201 3 16381561 16391699 - mRNA protein_coding 19 | -84350 ensorlt00000005743 sorlg00000004567 lims1-202 3 16381561 16389737 - mRNA protein_coding 20 | 90475 ensorlt00000006142 sorlg00000004873 rasa3-201 3 16519928 16565451 - mRNA protein_coding 21 | 97022 ensorlt00000006230 sorlg00000004938 tpp2-201 3 16571998 16592453 + mRNA protein_coding 22 | 97022 ensorlt00000044630 sorlg00000004938 tpp2-202 3 16571998 16592453 + mRNA protein_coding 23 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0043_chr23-3850204-3850968.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 8784 ensorlt00000011959 sorlg00000009536 arntl2-201 23 3833810 3859752 - mRNA protein_coding 3 | 8784 ensorlt00000032665 sorlg00000009536 arntl2-202 23 3833810 3859752 - mRNA protein_coding 4 | 46922 ensorlt00000012001 sorlg00000009571 stk38l-201 23 3873153 3897890 - mRNA protein_coding 5 | 46922 ensorlt00000012007 sorlg00000009571 stk38l-202 23 3875745 3897890 - mRNA protein_coding 6 | -48877 ensorlt00000035758 sorlg00000029239 zgc:162331-201 23 3801327 3824145 + mRNA protein_coding 7 | 60500 ensorlt00000012038 sorlg00000009602 fgfr1op2-201 23 3911468 3921194 + mRNA protein_coding 8 | -61094 ensorlt00000027106 sorlg00000025248 slc13a4-201 23 3730292 3789110 - mRNA protein_coding 9 | 61608 ensorlt00000012011 sorlg00000009581 med21-201 23 3904371 3912576 - mRNA protein_coding 10 | 72048 ensorlt00000012054 sorlg00000009613 tm7sf3-201 23 3923016 3937541 + mRNA protein_coding 11 | -74846 ensorlt00000034685 sorlg00000025248 slc13a4-202 23 3730433 3775358 - mRNA protein_coding 12 | 99061 ensorlt00000038268 sorlg00000009624 gas2l3-201 23 3935202 3950029 - mRNA protein_coding 13 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0044_chr15-29821056-29822141.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -11292 ensorlt00000037347 sorlg00000013714 mypn-202 15 29809764 29838754 + mRNA protein_coding 3 | -11292 ensorlt00000035168 sorlg00000013714 mypn-203 15 29809764 29838754 + mRNA protein_coding 4 | -11292 ensorlt00000017205 sorlg00000013714 mypn-201 15 29809764 29838754 + mRNA protein_coding 5 | 17090 ensorlt00000017211 sorlg00000013722 atoh7-201 15 29839231 29839659 + mRNA protein_coding 6 | -18728 ensorlt00000017149 sorlg00000013671 cacul1-201 15 29802328 29808402 + mRNA protein_coding 7 | 20648 ensorlt00000017221 sorlg00000013731 pkd2l1-201 15 29842789 29847677 + mRNA protein_coding 8 | 20648 ensorlt00000017223 sorlg00000013731 pkd2l1-202 15 29842789 29847999 + mRNA protein_coding 9 | -28511 ensorlt00000017134 sorlg00000013658 dnajc12-201 15 29787347 29792545 - mRNA protein_coding 10 | -28829 ensorlt00000017143 sorlg00000013667 15 29792227 29801391 + mRNA protein_coding 11 | -33914 ensorlt00000033992 sorlg00000025762 metazoa_srp-201 15 29786845 29787142 - ncRNA misc_rna 12 | -34986 ensorlt00000017128 sorlg00000013653 cox5b2-201 15 29785198 29786070 - mRNA protein_coding 13 | 36383 ensorlt00000027004 sorlg00000013798 tial1-201 15 29849827 29858524 - mRNA protein_coding 14 | 36383 ensorlt00000017307 sorlg00000013798 tial1-202 15 29848339 29858524 - mRNA protein_coding 15 | 37696 ensorlt00000036338 sorlg00000027170 bag3-201 15 29859837 29865589 + mRNA protein_coding 16 | 43469 ensorlt00000017395 sorlg00000013866 inpp5f-202 15 29865610 29873585 + mRNA protein_coding 17 | 43469 ensorlt00000017392 sorlg00000013866 inpp5f-201 15 29865610 29873585 + mRNA protein_coding 18 | -48053 ensorlt00000017115 sorlg00000013638 herc4-202 15 29773003 29787214 + mRNA protein_coding 19 | -48053 ensorlt00000017121 sorlg00000013638 herc4-201 15 29773003 29787214 + mRNA protein_coding 20 | -57841 ensorlt00000016953 sorlg00000013521 15 29763215 29768046 + mRNA protein_coding 21 | -64884 ensorlt00000044944 sorlg00000029445 15 29756172 29764994 + mRNA protein_coding 22 | 65067 ensorlt00000029995 sorlg00000029085 mcmbp-201 15 29875471 29887208 - mRNA protein_coding 23 | 65634 ensorlt00000017438 sorlg00000013906 sec23ip-202 15 29887775 29893715 + mRNA protein_coding 24 | 65634 ensorlt00000027553 sorlg00000013906 sec23ip-201 15 29887775 29893003 + mRNA protein_coding 25 | -75452 ensorlt00000029317 sorlg00000026320 mlh1-201 15 29738504 29745604 - mRNA protein_coding 26 | 78662 ensorlt00000017461 sorlg00000013924 csgalnact2-201 15 29894615 29900803 - mRNA protein_coding 27 | 79921 ensorlt00000017463 sorlg00000013924 csgalnact2-202 15 29894615 29902062 - mRNA protein_coding 28 | 92861 ensorlt00000031097 sorlg00000013965 ret-202 15 29902694 29915002 - mRNA protein_coding 29 | 96006 ensorlt00000017509 sorlg00000013965 ret-201 15 29902694 29918147 - mRNA protein_coding 30 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0045_chr13-383208-383975.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 485 ensorlt00000032832 sorlg00000027102 sst1.1-201 13 383149 384460 - mRNA protein_coding 3 | 8660 ensorlt00000023877 sorlg00000019158 13 390875 392635 - mRNA protein_coding 4 | -48030 ensorlt00000025754 sorlg00000020795 ece2b-201 13 311411 335178 - mRNA protein_coding 5 | -58067 ensorlt00000045877 sorlg00000020795 ece2b-202 13 311411 325141 - mRNA protein_coding 6 | 81199 ensorlt00000044286 sorlg00000025981 13 465174 475493 + mRNA protein_coding 7 | -82631 ensorlt00000025751 sorlg00000020793 spcs2-201 13 296602 300577 - mRNA protein_coding 8 | -88352 ensorlt00000033931 sorlg00000020791 abcg1-201 13 285578 294856 - mRNA protein_coding 9 | -88352 ensorlt00000025749 sorlg00000020791 abcg1-202 13 286195 294856 - mRNA protein_coding 10 | 91967 ensorlt00000036422 sorlg00000029571 13 475942 477534 + mRNA protein_coding 11 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0046_chr8-21261846-21262796.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -5983 ensorlt00000024432 sorlg00000019647 8 21228342 21255863 - mRNA protein_coding 3 | 8751 ensorlt00000033250 sorlg00000028274 8 21262451 21271547 - mRNA protein_coding 4 | -12904 ensorlt00000033251 sorlg00000021901 8 21242553 21248942 - mRNA protein_coding 5 | 28819 ensorlt00000045984 sorlg00000029111 8 21290979 21291615 - mRNA protein_coding 6 | -40524 ensorlt00000045769 sorlg00000027952 8 21205933 21221322 - mRNA protein_coding 7 | 47704 ensorlt00000033292 sorlg00000023163 8 21305685 21310500 - mRNA protein_coding 8 | 50182 ensorlt00000038496 sorlg00000025742 8 21312342 21312978 - mRNA protein_coding 9 | -61227 ensorlt00000028784 sorlg00000030111 kri1-201 8 21196606 21200619 - mRNA protein_coding 10 | -62098 ensorlt00000046048 sorlg00000030111 kri1-202 8 21196606 21199748 - mRNA protein_coding 11 | -64307 ensorlt00000046023 sorlg00000026945 8 21197443 21197539 - snoRNA snorna 12 | -72728 ensorlt00000043118 sorlg00000025827 8 21186862 21189118 - mRNA protein_coding 13 | -75704 ensorlt00000019278 sorlg00000015403 kri1-201 8 21182995 21186142 - mRNA protein_coding 14 | 75752 ensorlt00000029478 sorlg00000023163 8 21284835 21338548 - mRNA protein_coding 15 | -79892 ensorlt00000030195 sorlg00000015391 spc24-201 8 21178813 21181954 - mRNA protein_coding 16 | -79892 ensorlt00000019265 sorlg00000015391 spc24-202 8 21178813 21181954 - mRNA protein_coding 17 | 80251 ensorlt00000027038 sorlg00000022846 8 21319440 21343047 - mRNA protein_coding 18 | -86912 ensorlt00000019249 sorlg00000015375 s1pr5a-201 8 21174934 21176061 + mRNA protein_coding 19 | 90707 ensorlt00000033586 sorlg00000025256 8 21349146 21353503 - mRNA protein_coding 20 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0047_chr10-1395471-1396245.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -24754 ensorlt00000030488 sorlg00000026262 10 1370717 1371853 + mRNA protein_coding 3 | 54543 ensorlt00000025138 sorlg00000020270 gask1b-201 10 1450788 1461500 + mRNA protein_coding 4 | -69835 ensorlt00000042201 sorlg00000020233 rxfp1-203 10 1182501 1325636 - mRNA protein_coding 5 | -69901 ensorlt00000025094 sorlg00000020233 rxfp1-204 10 1182702 1325570 - mRNA protein_coding 6 | -75696 ensorlt00000036112 sorlg00000020235 10 1314901 1319775 - mRNA protein_coding 7 | -75824 ensorlt00000045286 sorlg00000020235 10 1314901 1319647 - mRNA protein_coding 8 | -75904 ensorlt00000044074 sorlg00000020235 10 1314901 1319567 - mRNA protein_coding 9 | -76926 ensorlt00000039896 sorlg00000020235 10 1314901 1318545 - mRNA protein_coding 10 | -77161 ensorlt00000027450 sorlg00000020235 10 1314901 1318310 - mRNA protein_coding 11 | -77587 ensorlt00000038461 sorlg00000020235 10 1314901 1317884 - mRNA protein_coding 12 | -77849 ensorlt00000046876 sorlg00000020235 10 1314901 1317622 - mRNA protein_coding 13 | -78203 ensorlt00000027419 sorlg00000020235 10 1314901 1317268 - mRNA protein_coding 14 | -78781 ensorlt00000025096 sorlg00000020235 10 1314901 1316690 - mRNA protein_coding 15 | -79006 ensorlt00000041303 sorlg00000020235 10 1314901 1316465 - mRNA protein_coding 16 | 79038 ensorlt00000025127 sorlg00000020262 tmem144b-201 10 1444958 1475283 - mRNA protein_coding 17 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0048_chr23-22979232-22979976.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 2437 ensorlt00000021719 sorlg00000017367 kcnmb4-201 23 22982413 23003483 + mRNA protein_coding 3 | -13041 ensorlt00000021713 sorlg00000017361 cnot2-203 23 22966191 22973692 + mRNA protein_coding 4 | -15938 ensorlt00000035794 sorlg00000017361 cnot2-202 23 22963294 22978404 + mRNA protein_coding 5 | -17795 ensorlt00000037938 sorlg00000023963 23 22957103 22961437 - mRNA protein_coding 6 | -18102 ensorlt00000040908 sorlg00000017361 cnot2-201 23 22961130 22978404 + mRNA protein_coding 7 | -20927 ensorlt00000042228 sorlg00000027073 23 22958305 22963215 + mRNA protein_coding 8 | -47154 ensorlt00000021697 sorlg00000017348 dyrk2-201 23 22932078 22949529 + mRNA protein_coding 9 | -48037 ensorlt00000021692 sorlg00000017343 23 22919415 22931195 - mRNA protein_coding 10 | -59710 ensorlt00000021688 sorlg00000017339 23 22907221 22919522 - mRNA protein_coding 11 | 67450 ensorlt00000033926 sorlg00000017385 ptprb-201 23 23020146 23047426 - mRNA protein_coding 12 | 74051 ensorlt00000046123 sorlg00000017385 ptprb-203 23 23021292 23054027 - mRNA protein_coding 13 | 74587 ensorlt00000021744 sorlg00000017385 ptprb-202 23 23021292 23054563 - mRNA protein_coding 14 | -75275 ensorlt00000043668 sorlg00000017329 23 22892799 22903957 - mRNA protein_coding 15 | -75275 ensorlt00000028700 sorlg00000017329 23 22892963 22903957 - mRNA protein_coding 16 | -75275 ensorlt00000021675 sorlg00000017329 23 22892799 22903957 - mRNA protein_coding 17 | -75275 ensorlt00000035791 sorlg00000017329 23 22892799 22903957 - mRNA protein_coding 18 | -85103 ensorlt00000044338 sorlg00000028312 23 22894129 22895715 + mRNA protein_coding 19 | 94486 ensorlt00000021748 sorlg00000017389 ptprr-201 23 23054584 23074462 - mRNA protein_coding 20 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0049_chr16-27924435-27925464.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | -741 ensorlt00000037928 sorlg00000029845 rnf183-201 16 27923694 27929922 + mRNA protein_coding 3 | 7518 ensorlt00000020012 sorlg00000015989 mgat1a-201 16 27932982 27936971 + mRNA protein_coding 4 | 10694 ensorlt00000033057 sorlg00000015993 sh3bp5la-201 16 27936158 27941996 + mRNA protein_coding 5 | 11277 ensorlt00000020018 sorlg00000015993 sh3bp5la-202 16 27936741 27940398 + mRNA protein_coding 6 | -13582 ensorlt00000030804 sorlg00000015982 dhx16-202 16 27910853 27923169 + mRNA protein_coding 7 | -15341 ensorlt00000020006 sorlg00000015982 dhx16-201 16 27909094 27923169 + mRNA protein_coding 8 | -19363 ensorlt00000019975 sorlg00000015959 16 27898998 27905072 - mRNA protein_coding 9 | -19363 ensorlt00000031499 sorlg00000015959 16 27898998 27905072 - mRNA protein_coding 10 | 22589 ensorlt00000020060 sorlg00000016024 16 27948053 28004636 + mRNA protein_coding 11 | -25476 ensorlt00000030881 sorlg00000024124 16 27893261 27898959 - mRNA protein_coding 12 | -26473 ensorlt00000041871 sorlg00000024124 16 27893261 27897962 - mRNA protein_coding 13 | -27172 ensorlt00000037695 sorlg00000024124 16 27893261 27897263 - mRNA protein_coding 14 | -31387 ensorlt00000046043 sorlg00000030371 16 27839676 27893048 - mRNA protein_coding 15 | -31387 ensorlt00000038902 sorlg00000030371 16 27839676 27893048 - mRNA protein_coding 16 | -39381 ensorlt00000031722 sorlg00000022507 16 27877300 27885054 - mRNA protein_coding 17 | -41962 ensorlt00000043601 sorlg00000022507 16 27872858 27882473 - mRNA protein_coding 18 | -52325 ensorlt00000036076 sorlg00000025297 16 27869554 27872110 - mRNA protein_coding 19 | -52998 ensorlt00000030249 sorlg00000025297 16 27869554 27871437 - mRNA protein_coding 20 | -55104 ensorlt00000044300 sorlg00000030371 16 27839676 27869331 - mRNA protein_coding 21 | -59933 ensorlt00000030765 sorlg00000029591 16 27859711 27864502 - mRNA protein_coding 22 | -62013 ensorlt00000028071 sorlg00000029591 16 27861331 27862422 - mRNA protein_coding 23 | -77607 ensorlt00000044512 sorlg00000030371 16 27839676 27846828 - mRNA protein_coding 24 | -86590 ensorlt00000043263 sorlg00000030239 si:ch73-95l15.5-201 16 27830553 27837845 - mRNA protein_coding 25 | 87355 ensorlt00000046524 sorlg00000022264 16 28009076 28012819 - mRNA protein_coding 26 | -95154 ensorlt00000028300 sorlg00000028753 ccdc105-201 16 27817164 27829281 - mRNA protein_coding 27 | -------------------------------------------------------------------------------- /docs/Comp_Report/medaka_html/interval_tables/interval_0050_chr21-28550521-28551558.tsv: -------------------------------------------------------------------------------- 1 | distance to tss transcript id gene id transcript name chromosome start end strand feature type transcript biotype 2 | 408 ensorlt00000040597 sorlg00000018243 pgap1-202 21 28551966 28564640 + mRNA protein_coding 3 | -713 ensorlt00000044798 sorlg00000022432 21 28548687 28549808 - mRNA protein_coding 4 | -3149 ensorlt00000022850 sorlg00000018243 pgap1-201 21 28547372 28564640 + mRNA protein_coding 5 | -3170 ensorlt00000024708 sorlg00000028215 tyw5-202 21 28540095 28547351 - mRNA protein_coding 6 | -6914 ensorlt00000022842 sorlg00000018239 maip1-201 21 28543607 28547351 + mRNA protein_coding 7 | -7231 ensorlt00000042490 sorlg00000028215 tyw5-201 21 28538633 28543290 - mRNA protein_coding 8 | -29054 ensorlt00000031131 sorlg00000024134 21 28521467 28538559 + mRNA protein_coding 9 | -44392 ensorlt00000043255 sorlg00000024134 21 28506129 28538612 + mRNA protein_coding 10 | -44392 ensorlt00000035063 sorlg00000024134 21 28506129 28538612 + mRNA protein_coding 11 | -44392 ensorlt00000022840 sorlg00000024134 21 28506129 28538612 + mRNA protein_coding 12 | 48370 ensorlt00000027731 sorlg00000026117 21 28599928 28605326 + mRNA protein_coding 13 | -61655 ensorlt00000022839 sorlg00000018237 21 28484059 28488866 - mRNA protein_coding 14 | -80812 ensorlt00000030616 sorlg00000026425 21 28468358 28469709 - mRNA protein_coding 15 | -------------------------------------------------------------------------------- /docs/Comp_Report/usage.md: -------------------------------------------------------------------------------- 1 | # Meth_Comp usage 2 | 3 | **Generate a fully responsive interactive HTML report for significant differentially methylated intervals found with `pycoMeth Meth_Comp`.** 4 | **At the moment only data binned by intervals with `Interval_Aggregate` are supported.** 5 | 6 | ## Example usage 7 | 8 | * [Python API usage](https://a-slide.github.io/pycoMeth/Comp_Report/API_usage/) 9 | * [Shell CLI usage](https://a-slide.github.io/pycoMeth/Comp_Report/CLI_usage/) 10 | 11 | ## Input files 12 | 13 | ### pycoMeth CpG_Aggregate or Interval_Aggregate output file 14 | 15 | A **TSV** output files generated with `pycoMeth Meth_comp` with data binned by intervals using `pycoMeth Interval_Aggregate`. 16 | 17 | ### Reference GFF3 file 18 | 19 | An **Ensembl GFF3** file containing genomic annotations to extract transcripts with TSS close to the top most significant CpG Intervals. 20 | 21 | * Main Ensembl: https://www.ensembl.org/index.html 22 | * Ensembl Bacteria: http://bacteria.ensembl.org/index.html 23 | * Ensembl Fungi: http://fungi.ensembl.org/index.html 24 | * Ensembl Plants: http://plants.ensembl.org/index.html 25 | * Ensembl Protists: http://protists.ensembl.org/index.html 26 | * Ensembl Metazoa: http://metazoa.ensembl.org/index.html 27 | 28 | ### Reference FASTA file 29 | 30 | FASTA reference file used for read alignment and Nanopolish. This file is required and used to sort the chromosomes in the ideogram plot. 31 | 32 | ## Output files 33 | 34 | ### Summary HTML report (pycoMeth_summary_report.html) 35 | 36 | Entry point to the report containing information of methylation status at genomic level. 37 | 38 | [Example Summary report](https://a-slide.github.io/pycoMeth/Comp_Report/medaka_html/pycoMeth_summary_report.html) 39 | 40 | The report contains the following items: 41 | 42 | * Overall summary 43 | Simple table containing counts of intervals and CpGs significantly differentially methylated. 44 | 45 | * Methylation category counts by sample 46 | Interactive plotly stacked bar plot showing the number of methylated, unmethylated and ambiguous intervals for each samples. 47 | 48 | * Methylation log-likelihood ratio by CpG interval 49 | Interactive plotly heatmap of the median llr for all significant intervals. 50 | Sites are ordered by genomic coordinates and samples are clustered by hierarchical clustering. 51 | 52 | * Distribution of CpG methylation log-likelihood ratio by sample 53 | Interactive plotly ridgeplot of median llr distribution for all sample at interval resolution. 54 | Samples are ordered by descending overall median llr. 55 | 56 | * Ideogram of the distribution of significant CpG intervals by chromosomic intervals 57 | 58 | Interactive chromosome ideogram plot showing the number of significant sites binned in large intervals. 59 | 60 | * Top differentially methylated intervals 61 | Table containing details of the n top differentially methylated candidates ranked by adjusted pvalue. 62 | The table contains links to individual intervals HTML reports. 63 | 64 | ### Top intervals HTML reports 65 | 66 | Individual reports for the top differentially methylated interval candidates. 67 | The right side navigation bar allows to explore all the other intervals or go back to the summary report. 68 | 69 | [Example Interval report](https://a-slide.github.io/pycoMeth/Comp_Report/medaka_html/interval_reports/interval_0001_chr15-13014693-13015794.html) 70 | 71 | The report contains the following items: 72 | 73 | * Interval details 74 | Simple table containing details about the interval 75 | 76 | * Methylation log-likelihood ratio by CpG position 77 | Interactive plotly heatmap of the median llr for all CpG positions in the interval. 78 | Sites are ordered by genomic coordinates and samples are clustered by hierarchical clustering. 79 | 80 | * Distribution of CpG methylation log-likelihood ratio by sample 81 | Interactive plotly ridgeplot of median llr distribution for all sample at CpG resolution. 82 | Samples are ordered by descending overall median llr. 83 | 84 | * Closest transcripts TSS 85 | Table containing the list of all transcripts having their TSS within 100kb of the interval edges. 86 | Transcripts are ranked by TSS distance to the interval 87 | -------------------------------------------------------------------------------- /docs/Comp_Report/yeast_html/pycoMeth_summary_intervals.tsv: -------------------------------------------------------------------------------- 1 | pvalue chromosome start end Number of nearby TSS closest tx id closest tx name closest tx biotype distance to tss 2 | 0.029563770441734687 V 65380 65612 110 yel048c_m tca17 protein_coding -213 3 | -------------------------------------------------------------------------------- /docs/CpG_Aggregate/usage.md: -------------------------------------------------------------------------------- 1 | # CpG_Aggregate usage 2 | 3 | **Calculate methylation frequency at genomic CpG sites from the output of `nanopolish call-methylation`** 4 | 5 | ## Example usage 6 | 7 | * [Python API usage](https://a-slide.github.io/pycoMeth/CpG_Aggregate/API_usage/) 8 | * [Shell CLI usage](https://a-slide.github.io/pycoMeth/CpG_Aggregate/CLI_usage/) 9 | 10 | ## Input files 11 | 12 | ### Nanopolish call-methylation output file 13 | 14 | [`Nanopolish call-methylation`](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) tsv output file or a list of files or a regex matching several files. 15 | 16 | ### Reference FASTA file 17 | 18 | FASTA reference file used for read alignment and Nanopolish. This file is required and used to sort the CpG sites by coordinates 19 | 20 | ## Output files 21 | 22 | ### Tabulated TSV file 23 | 24 | This tabulated file contains the following fields: 25 | 26 | * chromosome / start / end: Genomic coordinates of the CpG or cluster of CpGs if in less than 5 bases from each other. 27 | * sequence: -5 to +5 sequence of the motif or group of motifs in case split_group was not selected. 28 | * num_motifs: Number of motifs (CpG) found in the cluster. 29 | * median_llr: Median of log likelihood ratios for all read mapped 30 | * llr_list: List of raw llr values 31 | 32 | ### BED file 33 | 34 | Standard genomic [BED9 format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) including an RGB color field. The score correspond to the median log likelihood ratio. 35 | The file is already sorted by coordinates and can be rendered with a genome browser such as IGV 36 | 37 | The sites are color-coded as follow: 38 | 39 | - Median log likelihood ratio higher than 2 (Methylated): Colorscale from orange (llr = 2) to deep red (llr >=6) 40 | - Median log likelihood ratio lower than 2 (Unmethylated): Colorscale from green (llr = -2) to deep blue (llr <= -6) 41 | - Grey: Median log likelihood ration between -2 and 2 (ambiguous methylation status) 42 | 43 | Here is an example of multiple methylation bed files rendered with IGV 44 | 45 | ![Example Bed Files](../pictures/CpG_Aggregate_2.png) 46 | -------------------------------------------------------------------------------- /docs/Interval_Aggregate/usage.md: -------------------------------------------------------------------------------- 1 | # Interval_Aggregate usage 2 | 3 | **Bin the output of `pycoMeth CpG_Aggregate` in genomic intervals, using either an annotation file containing interval or a sliding window.** 4 | 5 | ## Example usage 6 | 7 | * [Python API usage](https://a-slide.github.io/pycoMeth/Interval_Aggregate/API_usage/) 8 | * [Shell CLI usage](https://a-slide.github.io/pycoMeth/Interval_Aggregate/CLI_usage/) 9 | 10 | ## Input files 11 | 12 | ### pycoMeth CpG_Aggregate output file 13 | 14 | `pycoMeth CpG_Aggregate` **tsv** output file (not the bed output). 15 | 16 | ### Reference FASTA file 17 | 18 | FASTA reference file used for read alignment and Nanopolish. This file is required and used to sort the CpG sites by coordinates 19 | 20 | ### BED file containing intervals 21 | 22 | Optional **sorted** and BED file containing **non-overlapping** intervals to bin CpG data into. If this file is not provided, then the program use a sliding customizable window to bin data along the entire genome. 23 | 24 | ## Output files 25 | 26 | ### Tabulated TSV file 27 | 28 | This tabulated file contains the following fields: 29 | 30 | * chromosome / start / end : Genomic coordinates of the interval containing CpGs 31 | * num_motifs: Number of CpG positions/cluster found in the interval 32 | * median_llr: Median of all log likelihood ratios (llr) for the interval 33 | * llr_list: List of median llr values of all CpG positions/cluster found in the interval 34 | * pos_list: List of genomic coordinates of the center of all CpG positions/cluster found. The order matches values in llr_list 35 | 36 | ### BED file 37 | 38 | Standard genomic [BED9 format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) including an RGB color field. The score correspond to the median log likelihood ratio. 39 | The file is already sorted by coordinates and can be rendered with a genome browser such as IGV 40 | 41 | The sites are color-coded as follow: 42 | 43 | * Median log likelihood ratio higher than 2 (Methylated): Colorscale from orange (llr = 2) to deep red (llr >=6) 44 | * Median log likelihood ratio lower than 2 (Unmethylated): Colorscale from green (llr = -2) to deep blue (llr <= -6) 45 | * Grey: Median log likelihood ration between -2 and 2 (ambiguous methylation status) 46 | 47 | Here is an example of multiple methylation bed files rendered with IGV 48 | 49 | ![Example Bed Files](../pictures/Interval_Aggregate_2.png) 50 | -------------------------------------------------------------------------------- /docs/Meth_Comp/usage.md: -------------------------------------------------------------------------------- 1 | # Meth_Comp usage 2 | 3 | **Compare methylation values for each CpG positions (`pycoMeth CpG_Aggregate`) or intervals (`pycoMeth Interval_Aggregate`) between n samples and perform a statistical test to evaluate if the positions are significantly different. For 2 samples a Mann_Withney test is performed otherwise a Kruskal Wallis test is performed for multiple samples. pValues are adjusted for multiple tests using the Benjamini & Hochberg procedure for controlling the false discovery rate.** 4 | 5 | ## Example usage 6 | 7 | * [Python API usage](https://a-slide.github.io/pycoMeth/Meth_Comp/API_usage/) 8 | * [Shell CLI usage](https://a-slide.github.io/pycoMeth/Meth_Comp/CLI_usage/) 9 | 10 | ## Input files 11 | 12 | ### pycoMeth CpG_Aggregate or Interval_Aggregate output file 13 | 14 | A list of `pycoMeth CpG_Aggregate` or `pycoMeth Interval_Aggregate` **tsv** output files corresponding to different samples. 15 | 16 | ### Reference FASTA file 17 | 18 | FASTA reference file used for read alignment and Nanopolish. This file is required and used to sort the CpG sites by coordinates. 19 | 20 | ## Output files 21 | 22 | ### Tabulated TSV file 23 | 24 | By default this file contains all the sites found in a least one of the source CpG/interval aggregate file. This tabulated file contains the following fields: 25 | 26 | * chromosome / start / end / strand: Genomic coordinates of the CpG/interval containing CpGs 27 | * n_samples: Number of valid samples in the CpG/interval 28 | * pvalue: pvalue of the interval obtained by Kruskal Wallis or Mann_Withney test 29 | * adj_pvalue: FDR adjusted pvalue using the Benjamini & Hochberg procedure 30 | * neg_med / pos_med / ambiguous_med: Number of samples with a median below the negative llr threshold / above the positive llr threshold or with and ambiguous median between the 2 thresholds 31 | * [optional] unique_cpg_pos: Number of CpG position for which at least samples has valid data. ONLY if Meth_Comp was ran from files generated with Interval_Aggregate. 32 | * labels: labels of the samples tested, matching the order of values in med_llr_list and raw_llr_list 33 | * med_llr_list: List of median llr values for each samples compared. 34 | * raw_llr_list: List of lists of raw llr values for each samples compared 35 | * [optional] raw_pos_list: List of lists of genomic coordinates of the center of all CpG positions/clusters found for each samples compared. The order matches values in llr_list. ONLY if Meth_Comp was ran from files generated with Interval_Aggregate. 36 | And at last a comment field 37 | * comment: Can take one of the following self explanatory values: `Insufficient samples`, `Insufficient effect size`, `Non-significant pvalue` or `Significant pvalue` 38 | 39 | ### BED file 40 | 41 | Standard genomic [BED9 format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) including an RGB color field. The score correspond to the -log10(Adjusted Pvalue) capped to 1000. The file is sorted by coordinates and can be rendered with a genome browser such as IGV. 42 | 43 | The sites are color-coded as follow: 44 | 45 | * Significant differential methylation Adjusted pValue: Colorscale from orange (pValue=0.01) to deep purple (pValue<=0.000001) 46 | * Non-significant: Grey 47 | 48 | Here is an example of multiple methylation bed files rendered with IGV 49 | 50 | ![Example Bed Files](../pictures/Meth_Comp.png) 51 | -------------------------------------------------------------------------------- /docs/changelog.md: -------------------------------------------------------------------------------- 1 | ../CHANGELOG.md -------------------------------------------------------------------------------- /docs/code_of_conduct.md: -------------------------------------------------------------------------------- 1 | ../CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /docs/contributing.md: -------------------------------------------------------------------------------- 1 | ../CONTRIBUTING.md -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 | ![](pictures/pycoMeth_long.png) 2 | 3 | [![GitHub license](https://img.shields.io/github/license/a-slide/pycoMeth.svg)](https://github.com/a-slide/pycoMeth/blob/master/LICENSE) 4 | [![Language](https://img.shields.io/badge/Language-Python3-yellow.svg)](https://www.python.org/) 5 | [![PyPI version](https://badge.fury.io/py/pycoMeth.svg)](https://badge.fury.io/py/pycoMeth) 6 | [![PyPI downloads](https://pepy.tech/badge/pycoMeth)](https://pepy.tech/project/pycoMeth) 7 | [![DOI](https://zenodo.org/badge/211195001.svg)](https://zenodo.org/badge/latestdoi/211195001) 8 | [![Build Status](https://travis-ci.com/a-slide/pycoMeth.svg?branch=master)](https://travis-ci.com/a-slide/pycoMeth) 9 | 10 | --- 11 | 12 | # Welcome to pycoMeth documentation 13 | 14 | --- 15 | 16 | **DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets** 17 | 18 | `pycoMeth` can be used for further analyses starting from the output files generated by [`Nanopolish call-methylation`](https://github.com/jts/nanopolish). The package contains a suite of tools to **find CpG islands** calculate the **methylation probability at CpG dinucleotide or CpG island resolution** across the entire genome and to perform a **differential methylation analysis** across multiple samples. Finally an **interactive HTML report** can be generated to visualize significant intervals. 19 | 20 | The package contains the following modules: 21 | 22 | * [CGI_Finder](CGI_Finder/usage): Find CpG islands in a fasta file by using a sliding window and merging overlapping windows satisfying the CpG island definition. 23 | * [CpG_Aggregate](CpG_Aggregate/usage): Aggregate the output of `nanopolish call-methylation` at genomic position level. 24 | * [Interval_Aggregate](Interval_Aggregate/usage): Bin the output of `pycoMeth CpG_Aggregate` in genomic intervals, using either an annotation file or a sliding window. 25 | * [Meth_Comp](Meth_Comp/usage): Compare Methylation level between several samples from either `pycoMeth CpG_Aggregate` or `pycoMeth Interval_Aggregate`. 26 | * [Comp_Report](Comp_Report/usage): Generate an interactive HTML report for top significant differentially methylated intervals found with `pycoMeth Meth_Comp` 27 | 28 | `pycoMeth` generates extensive tabulated reports and BED files which can be loaded in a genome browser. In addition, an interactive HTML report of differentially 29 | methylated intervals/islands can also generated at the end of the analysis. 30 | 31 | [`Methplotlib`](https://github.com/wdecoster/methplotlib) developed by [Wouter de coster](https://twitter.com/wouter_decoster) is an excellent complementary tool to visualise and explore methylation status for specific loci. 32 | 33 | 34 | Please be aware that `pycoMeth` is a research package that is still under development. 35 | The API, command line interface, and implementation might change without retro-compatibility. 36 | 37 | --- 38 | 39 | ### pycoMeth workflow 40 | 41 | ![Workflow](pictures/pycoMeth_package.png) 42 | 43 | ### pycoMeth example output IGV rendering 44 | 45 | ![IGV](pictures/pycoMeth_all.png) 46 | 47 | ### pycoMeth example HTML report 48 | 49 | 50 | [Example HTML report 1](https://a-slide.github.io/pycoMeth/Comp_Report/medaka_html/pycoMeth_summary_report.html) 51 | 52 | [Example HTML report 2](https://a-slide.github.io/pycoMeth/Comp_Report/human_html/pycoMeth_summary_report.html) 53 | 54 | ![HTML](pictures/pycoMeth_HTML.gif) 55 | 56 | --- 57 | 58 | ### Citing 59 | 60 | The repository is archived at Zenodo. If you use `pycoMeth` please cite as follow: 61 | 62 | Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254 63 | 64 | ### Authors 65 | 66 | * Adrien Leger - aleg {at} ebi.ac.uk 67 | -------------------------------------------------------------------------------- /docs/installation.md: -------------------------------------------------------------------------------- 1 | # Installation 2 | 3 | ## Create a clean virtual environment (optional but recommended) 4 | 5 | Ideally, before installation, create a clean **python3.7+** virtual environment to deploy the package. 6 | Earlier version of Python3 should also work but **Python 2 is not supported**. 7 | For example one can use conda or virtualenvwrapper. 8 | 9 | With [virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/install.html): 10 | 11 | ```bash 12 | mkvirtualenv pycoMeth -p python3.7 13 | workon pycoMeth 14 | ``` 15 | 16 | With [conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html): 17 | 18 | ```bash 19 | conda create -n pycoMeth python=3.7 20 | conda activate pycoMeth 21 | ``` 22 | 23 | You might also want to install [Nanopolish](https://github.com/jts/nanopolish) in the same virtual environment so you can pipe nanopolish output directly into `pycoMeth` 24 | 25 | ## Dependencies 26 | 27 | [Nanopolish 0.10+](https://github.com/jts/nanopolish) is not a direct dependency but is required to generate the files used by several commands from this package 28 | 29 | `pycoMeth` relies on a the following robustly maintained third party python libraries: 30 | 31 | * `numpy>=1.14.0` 32 | * `scipy>=1.4.1` 33 | * `statsmodels>=0.11.1` 34 | * `pandas>=1.0.3` 35 | * `Jinja2>=2.11.1` 36 | * `plotly>=4.6.0` 37 | * `pyfaidx>=0.5.8` 38 | * `tqdm>=4.45.0` 39 | * `colorlog>=4.1.0` 40 | * `kaleido` *New library being developed by the plotly team for static image export* 41 | 42 | The correct versions of packages are installed together with the software when using pip or conda 43 | 44 | ## Option 1: Installation with pip from pypi 45 | 46 | Install or upgrade the package with pip from pypi 47 | 48 | ```bash 49 | pip install pycoMeth 50 | ``` 51 | 52 | You can also update to the **unstable** development version from test.pypi repository 53 | 54 | ```bash 55 | pip install --index-url https://test.pypi.org/simple/ pycoMeth -U 56 | ``` 57 | 58 | ## Option 2: Installation with conda from Anaconda cloud 59 | 60 | 61 | ```bash 62 | # First installation 63 | conda install -c aleg -c plotly pycometh 64 | ``` 65 | 66 | You can also get the **unstable** development version from the dev channel 67 | 68 | ```bash 69 | conda update -c aleg_dev -c plotly pycometh 70 | ``` 71 | 72 | ## Option 3: Installation with pip from Github 73 | 74 | Or from github to get the last version 75 | 76 | ```bash 77 | # First installation 78 | pip install git+https://github.com/a-slide/pycoMeth.git 79 | 80 | # First installation bleeding edge 81 | pip install git+https://github.com/a-slide/pycoMeth.git@dev 82 | 83 | # Update to last version 84 | pip install git+https://github.com/a-slide/pycoMeth.git --upgrade 85 | ``` 86 | 87 | ## Option 4: Clone the repository and install locally in develop mode 88 | 89 | With this option, the package will be locally installed in *editable* or *develop mode*. This allows the package to be both installed and editable in project form. This is the recommended option if you wish to modify the code and/or participate to the development of the package (see [contribution guidelines](contributing.md)). 90 | 91 | ```bash 92 | # Clone repo localy 93 | git clone https://github.com/a-slide/pycoMeth.git 94 | 95 | # Enter in repo directory 96 | cd pycoMeth 97 | 98 | # Make setup.py executable 99 | chmod u+x setup.py 100 | 101 | # Install with pip3 102 | pip3 install -e ./ 103 | ``` 104 | -------------------------------------------------------------------------------- /docs/licence.md: -------------------------------------------------------------------------------- 1 | ../LICENSE -------------------------------------------------------------------------------- /docs/pictures/CGI_Finder.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/a-slide/pycoMeth/9b7eeedea8a230039236597713ca4987066912d9/docs/pictures/CGI_Finder.png 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| run: 24 | - numpy>=1.14.0 25 | - scipy=1.4.1 26 | - statsmodels>=0.11.1 27 | - pandas>=1.0.3 28 | - Jinja2>=2.11.1 29 | - plotly=4.7.1 30 | - pyfaidx>=0.5.8 31 | - tqdm>=4.45.0 32 | - colorlog>=4.1.0 33 | 34 | test: 35 | imports: 36 | - pycoMeth.FileParser 37 | - pycoMeth.CoordGen 38 | - pycoMeth.CpG_Aggregate 39 | - pycoMeth.Interval_Aggregate 40 | - pycoMeth.Meth_Comp 41 | - pycoMeth.Comp_Report 42 | - pycoMeth.CGI_Finder 43 | commands: 44 | - pycoMeth CpG_Aggregate --help 45 | - pycoMeth Interval_Aggregate --help 46 | - pycoMeth Meth_Comp --help 47 | - pycoMeth Comp_Report --help 48 | - pycoMeth CGI_Finder --help 49 | 50 | about: 51 | home: "https://github.com/a-slide/pycoMeth" 52 | license: "GPL" 53 | summary: "DNA methylation analysis for Oxford Nanopore DNA sequencing datasets downstream to Nanopolish" 54 | -------------------------------------------------------------------------------- /mkdocs.yml: -------------------------------------------------------------------------------- 1 | # Required python packages to generate the documentation 2 | # * mkdocs 3 | # * mkdocs-material 4 | # * pygments 5 | # * pymdown-extensions 6 | # * mknotebooks 7 | 8 | # Project information 9 | site_name: 'pycoMeth' 10 | site_description: 'Python package for nanopore DNA methylation analysis downstream to Nanopolish' 11 | site_author: 'Adrien Leger' 12 | site_url: 'https://a-slide.github.io/pycoMeth/' 13 | 14 | # Repository 15 | repo_name: 'a-slide/pycoMeth' 16 | repo_url: 'https://github.com/a-slide/pycoMeth' 17 | 18 | # Copyright 19 | copyright: 'Copyright © 2019 Adrien Leger' 20 | 21 | # Navigation menu 22 | nav: 23 | - Home: index.md 24 | - Installation instructions: installation.md 25 | - CpG_Aggregate Usage: 26 | - Using CpG_Aggregate: CpG_Aggregate/usage.md 27 | - jupyter API usage: CpG_Aggregate/API_usage.ipynb 28 | - Command line usage: CpG_Aggregate/CLI_usage.ipynb 29 | - Interval_Aggregate Usage: 30 | - Using Interval_Aggregate: Interval_Aggregate/usage.md 31 | - jupyter API usage: Interval_Aggregate/API_usage.ipynb 32 | - Command line usage: Interval_Aggregate/CLI_usage.ipynb 33 | - Meth_Comp Usage: 34 | - Using Meth_Comp: Meth_Comp/usage.md 35 | - jupyter API usage: Meth_Comp/API_usage.ipynb 36 | - Command line usage: Meth_Comp/CLI_usage.ipynb 37 | - Comp_Report Usage: 38 | - Using Comp_Report: Comp_Report/usage.md 39 | - jupyter API usage: Comp_Report/API_usage.ipynb 40 | - Command line usage: Comp_Report/CLI_usage.ipynb 41 | - CGI_Finder Usage: 42 | - Using CGI_Finder: CGI_Finder/usage.md 43 | - jupyter API usage: CGI_Finder/API_usage.ipynb 44 | - Command line usage: CGI_Finder/CLI_usage.ipynb 45 | - Contributing: contributing.md 46 | - Code of conduct: code_of_conduct.md 47 | - Licence: licence.md 48 | - Changelog: changelog.md 49 | 50 | # Theme customization 51 | theme: 52 | name: 'material' 53 | highlightjs: true 54 | font: false 55 | 56 | markdown_extensions: 57 | - admonition 58 | - codehilite 59 | - pymdownx.betterem: 60 | smart_enable: all 61 | - pymdownx.caret 62 | - pymdownx.critic 63 | - pymdownx.details 64 | - pymdownx.emoji: 65 | emoji_generator: !!python/name:pymdownx.emoji.to_svg 66 | - pymdownx.inlinehilite 67 | - pymdownx.magiclink: 68 | repo_url_shorthand: true 69 | user: a-slide 70 | repo: pycoMeth 71 | - pymdownx.mark 72 | - pymdownx.smartsymbols 73 | - pymdownx.superfences 74 | - pymdownx.tasklist: 75 | custom_checkbox: true 76 | - pymdownx.tilde 77 | 78 | plugins: 79 | - mknotebooks 80 | -------------------------------------------------------------------------------- /pycoMeth/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | # Define self package variable 4 | __version__ = "0.4.25" 5 | __description__ = 'DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets' 6 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | 4 | from setuptools import setup 5 | 6 | # Define package info 7 | name = "pycoMeth" 8 | version = "0.4.25" 9 | description = "DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets" 10 | with open("README.md", "r") as fh: 11 | long_description = fh.read() 12 | 13 | # Collect info in a dictionnary for setup.py 14 | setup( 15 | name = name, 16 | description = description, 17 | version = version, 18 | long_description = long_description, 19 | long_description_content_type="text/markdown", 20 | url = "https://github.com/a-slide/pycoMeth", 21 | author = 'Adrien Leger', 22 | author_email = 'aleg@ebi.ac.uk', 23 | license= "GPL", 24 | python_requires ='>=3.6', 25 | classifiers = [ 26 | 'Development Status :: 3 - Alpha', 27 | 'Intended Audience :: Science/Research', 28 | 'Topic :: Scientific/Engineering :: Bio-Informatics', 29 | 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', 30 | 'Programming Language :: Python :: 3'], 31 | install_requires = [ 32 | "numpy>=1.14.0", 33 | "scipy==1.4.1", 34 | "statsmodels>=0.11.1", 35 | "pandas>=1.0.3", 36 | "Jinja2>=2.11.1", 37 | "plotly==4.7.1", 38 | "pyfaidx>=0.5.8", 39 | "tqdm>=4.45.0", 40 | "colorlog>=4.1.0"], 41 | packages = [name], 42 | package_dir = {name: name}, 43 | package_data = {name: ['templates/*']}, 44 | entry_points = {'console_scripts': ['pycoMeth=pycoMeth.__main__:main']}) 45 | --------------------------------------------------------------------------------