├── FileSplitter.py ├── LICENSE ├── README.md ├── accuracyTest ├── CalAccuracy.py ├── tdna10x_insertionBED.txt ├── tdna20x_insertionBED.txt ├── tdna40x_insertionBED.txt └── tdna5x_insertionBED.txt ├── example ├── mt4_chr1_20x_mut_tdna_1.fq ├── mt4_chr1_20x_mut_tdna_2.fq ├── mt4_chr1_2Mb.fa └── t-dna_elison.fa ├── simulation ├── TDNAInsert.py └── TDNATruncate.py ├── tdnaAnnot.py └── tdnascan.py /FileSplitter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/FileSplitter.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/README.md -------------------------------------------------------------------------------- /accuracyTest/CalAccuracy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/accuracyTest/CalAccuracy.py -------------------------------------------------------------------------------- /accuracyTest/tdna10x_insertionBED.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/accuracyTest/tdna10x_insertionBED.txt -------------------------------------------------------------------------------- /accuracyTest/tdna20x_insertionBED.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/accuracyTest/tdna20x_insertionBED.txt -------------------------------------------------------------------------------- /accuracyTest/tdna40x_insertionBED.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/accuracyTest/tdna40x_insertionBED.txt -------------------------------------------------------------------------------- /accuracyTest/tdna5x_insertionBED.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/accuracyTest/tdna5x_insertionBED.txt -------------------------------------------------------------------------------- /example/mt4_chr1_20x_mut_tdna_1.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/example/mt4_chr1_20x_mut_tdna_1.fq -------------------------------------------------------------------------------- /example/mt4_chr1_20x_mut_tdna_2.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/example/mt4_chr1_20x_mut_tdna_2.fq -------------------------------------------------------------------------------- /example/mt4_chr1_2Mb.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/example/mt4_chr1_2Mb.fa -------------------------------------------------------------------------------- /example/t-dna_elison.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/example/t-dna_elison.fa -------------------------------------------------------------------------------- /simulation/TDNAInsert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/simulation/TDNAInsert.py -------------------------------------------------------------------------------- /simulation/TDNATruncate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/simulation/TDNATruncate.py -------------------------------------------------------------------------------- /tdnaAnnot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/tdnaAnnot.py -------------------------------------------------------------------------------- /tdnascan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BCH-RC/TDNAscan/HEAD/tdnascan.py --------------------------------------------------------------------------------