├── pipelines ├── code ├── data ├── atacseq-standard │ ├── data │ ├── __02b-qc │ ├── __05a-pca │ ├── inputs │ │ ├── code │ │ ├── data │ │ └── genomes │ ├── pipeline │ │ ├── code │ │ ├── align │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.bowtie2.tcsh │ │ ├── inputs │ │ ├── pca │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrices │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── peaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ └── params │ │ │ │ ├── gsize.info.txt │ │ │ │ └── params.macs.broad.tcsh │ │ ├── qc │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.default.tcsh │ │ ├── code.main │ │ ├── diffbind │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ ├── params.norm_edger.tcsh │ │ │ │ └── params.norm_deseq2.tcsh │ │ ├── fastqc │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.fastqc.tcsh │ │ ├── heatmaps │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrices │ │ │ └── params │ │ │ │ ├── params.mean.tcsh │ │ │ │ └── params.standard.tcsh │ │ ├── matrices │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ ├── params.flank_500nt.nbins_1.tcsh │ │ │ │ ├── params.win_1kb.nbins_1.tcsh │ │ │ │ └── params.flank_2500nt.nbins_25.tcsh │ │ ├── nucleoatac │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.macs_broad.tcsh │ │ ├── peakanno │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── peaktable │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── align-stats │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── count_peaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── summ-peakanno │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── venn-diagram │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ └── index.txt │ ├── __01a-align │ ├── __03a-peaks │ ├── code.main │ ├── __02a-fastqc │ ├── __04a-matrices │ ├── __05c-peakanno │ ├── __06a-diffbind │ ├── report │ │ ├── pipeline │ │ ├── project_info.txt │ │ ├── figure │ │ │ └── NYU_white.jpg │ │ └── notes.tex │ ├── __03b-peaktable │ ├── __05b-heatmaps │ ├── code │ ├── __01b-align-stats │ ├── __04b-count-peaks │ ├── __05d-summ-peakanno │ ├── __05e-venn-diagram │ ├── project_notes │ │ └── Project_Notebook.Rmd │ └── project_info.txt ├── chipseq-standard │ ├── data │ ├── __02b-qc │ ├── __05a-pca │ ├── inputs │ │ ├── code │ │ ├── data │ │ └── genomes │ ├── pipeline │ │ ├── code │ │ ├── align │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.bowtie2.tcsh │ │ ├── inputs │ │ ├── pca │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrices │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── peaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ └── params │ │ │ │ └── gsize.info.txt │ │ ├── qc │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.default.tcsh │ │ ├── code.main │ │ ├── diffbind │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ ├── params.norm_edger.tcsh │ │ │ │ └── params.norm_deseq2.tcsh │ │ ├── fastqc │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.fastqc.tcsh │ │ ├── heatmaps │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrices │ │ │ └── params │ │ │ │ ├── params.mean.tcsh │ │ │ │ └── params.standard.tcsh │ │ ├── matrices │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ ├── params.flank_500nt.nbins_1.tcsh │ │ │ │ ├── params.win_1kb.nbins_1.tcsh │ │ │ │ └── params.flank_2500nt.nbins_25.tcsh │ │ ├── peakanno │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── peakdiff │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrices │ │ │ └── params │ │ │ │ ├── params.advanced.tcsh │ │ │ │ └── params.standard.tcsh │ │ ├── peaktable │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── align-stats │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── count_peaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── homer_findPeaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── inpdirs │ │ │ │ └── homer_tagdir │ │ ├── homer_motif │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── inpdirs │ │ │ │ └── peaks │ │ ├── homer_tagdir │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── inpdirs │ │ │ │ └── align │ │ │ └── clean.tcsh │ │ ├── summ-peakanno │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── peaks │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── venn-diagram │ │ │ ├── code │ │ │ ├── errors │ │ │ │ └── error.log │ │ │ ├── inputs │ │ │ ├── inpdirs │ │ │ │ ├── align │ │ │ │ └── peaks │ │ │ ├── clean.tcsh │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── homer_annotatepeaks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── inpdirs │ │ │ │ └── peaks │ │ ├── homer_superenhancer │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── inpdirs │ │ │ │ └── homer_tagdir │ │ └── index.txt │ ├── __01a-align │ ├── __03a-peaks │ ├── code.main │ ├── __02a-fastqc │ ├── __04a-matrices │ ├── __05c-peakanno │ ├── __06a-diffbind │ ├── report │ │ ├── pipeline │ │ ├── project_info.txt │ │ ├── figure │ │ │ └── NYU_white.jpg │ │ └── notes.tex │ ├── __03b-peaktable │ ├── __05b-heatmaps │ ├── code │ ├── __01b-align-stats │ ├── __03c-count_peaks │ ├── __05d-summ-peakanno │ ├── __05e-venn-diagram │ ├── project_notes │ │ └── Project_Notebook.Rmd │ └── project_info.txt └── hicseq-standard │ ├── data │ ├── inputs │ ├── inputs │ ├── code │ ├── data │ ├── genomes │ ├── create-sample-sheet.tcsh │ └── config-FitHiChIP │ │ └── configfile │ ├── pipeline │ ├── code │ ├── inputs │ ├── align │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ └── inputs │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ ├── read-sample-sheet.tcsh │ │ │ └── merge-bam-files.tcsh │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── menu │ │ │ ├── params.bowtie2.tcsh │ │ │ └── params.gtools.tcsh │ │ │ └── params.bwa.tcsh │ ├── annotations │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── interactions │ │ └── params │ │ │ └── params.standard.tcsh │ ├── cnv │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ └── scripts-hint-cnv.sh │ │ ├── inpdirs │ │ │ └── tracks │ │ └── params │ │ │ └── params.res_50kb.tcsh │ ├── code.main │ ├── domains │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── menu │ │ │ ├── params.armatus.gamma_005.tcsh │ │ │ ├── params.armatus.gamma_01.tcsh │ │ │ ├── params.armatus.gamma_02.tcsh │ │ │ ├── params.armatus.gamma_03.tcsh │ │ │ ├── params.armatus.gamma_05.tcsh │ │ │ ├── params.armatus.gamma_07.tcsh │ │ │ ├── params.topdom.win_3.tcsh │ │ │ ├── params.topdom.win_7.tcsh │ │ │ ├── params.crane.ins_1000K.tcsh │ │ │ ├── generate-param-scripts │ │ │ └── params.crane.ins_2000K.tcsh │ │ │ └── params.topdom.win_5.tcsh │ ├── filter │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ └── align │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ ├── hicseq-filter.tcsh │ │ │ ├── read-sample-sheet.tcsh │ │ │ └── peakCall.sh │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── menu │ │ │ ├── params.mapq_20.mindist_5000.tcsh │ │ │ ├── params.mapq_15.tcsh │ │ │ └── params.mapq_20.mindist25.tcsh │ │ │ └── params.mapq_20_mindist0.tcsh │ ├── hicplotter │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ ├── matrix-prep │ │ │ ├── matrix-hicnorm │ │ │ ├── matrix-distnorm │ │ │ └── matrix-estimated │ │ └── submit_step_run.sh │ ├── hubs │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.pipeline │ │ │ └── code.main │ │ ├── inpdirs │ │ │ └── loops │ │ └── params │ │ │ └── params.standard.tcsh │ ├── loops │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ └── filter │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ └── submit_step_run.sh │ ├── matrix-cnv │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-filtered │ │ └── params │ │ │ └── params.standard.tcsh │ ├── matrix-diff │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ ├── matrix-prep │ │ │ ├── matrix-estimated │ │ │ └── matrix-hicnorm │ │ └── params │ │ │ └── params.standard.tcsh │ ├── matrix-ic │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-filtered │ │ ├── submit_step_run.sh │ │ └── params │ │ │ └── params.cutoff_0.tcsh │ ├── matrix-prep │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-filtered │ │ └── params │ │ │ ├── menu │ │ │ ├── params.impute.tcsh │ │ │ ├── params.scale.tcsh │ │ │ └── params.scale_impute45.tcsh │ │ │ └── params.scale3.tcsh │ ├── tracks │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ └── filter │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── menu │ │ │ ├── params.washu.res_40kb.tcsh │ │ │ ├── params.h5.res_10kb.tcsh │ │ │ ├── params.h5.res_20kb.tcsh │ │ │ ├── params.cool.res_20kb.tcsh │ │ │ ├── params.ginteractions.res_10kb.tcsh │ │ │ ├── params.ginteractions.res_10kb_raw.tcsh │ │ │ └── params.cool.multires.tcsh │ │ │ └── params.juicer.tcsh │ ├── APA-diff │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ ├── filter │ │ │ └── tracks │ │ ├── submit_step_run.sh │ │ ├── instructions-run │ │ └── params │ │ │ ├── params.res_5kb.tcsh │ │ │ └── menu │ │ │ └── params.res_10kb.tcsh │ ├── boundary-diff │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ └── inpdirs │ │ │ ├── matrix-ic │ │ │ ├── matrix-prep │ │ │ └── matrix-estimated │ ├── boundary-scores │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── params.connectivity_2Mb.tcsh │ │ │ └── params.activity_500kb.tcsh │ ├── compare-matrices │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ ├── matrix-prep │ │ │ ├── matrix-estimated │ │ │ └── matrix-hicnorm │ │ └── params │ │ │ └── params.standard.tcsh │ ├── compartments │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ ├── hicseq-compartments.tcsh │ │ │ ├── hicseq-compartments-homer.tcsh │ │ │ └── CscoreTool1.1 │ │ ├── inpdirs │ │ │ └── filter │ │ ├── submit_step_run.sh │ │ └── params │ │ │ └── params.homer.res_100kb.tcsh │ ├── domains-diff │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── menu │ │ │ ├── params.topdom.win_5.cpm.common.tcsh │ │ │ ├── params.topdom.win_5.cpm.ref1.tcsh │ │ │ ├── params.hicratio.d_0500.cpm.common.tcsh │ │ │ ├── params.topdom.win_5.dist_norm.ref1.tcsh │ │ │ ├── params.topdom.win_5.dist_norm.common.tcsh │ │ │ └── params.hicratio.d_0500.dist_norm.common.tcsh │ │ │ ├── params.hicratio.d_0500.cpm.ref1.tcsh │ │ │ └── params.hicratio.d_0500.dist_norm.ref1.tcsh │ ├── domains-stats │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── domains │ │ ├── submit_step_run.sh │ │ └── params │ │ │ └── params.standard.tcsh │ ├── filter-resample │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── filter │ │ └── params │ │ │ └── params.reads_100M.tcsh │ ├── filter-stats │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ └── filter │ │ ├── params │ │ │ └── params.standard.tcsh │ │ └── submit_step_run.sh │ ├── hicplotter-diff │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ └── matrix-distnorm │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── params.hicratio-selected-regions.tcsh │ │ │ └── params.topdom-selected-regions.tcsh │ ├── hubs-stats │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ ├── loops │ │ │ ├── virtual4C │ │ │ └── virtual5C │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── submit_run-v5c.sh │ │ └── submit_run-fithic.sh │ ├── interactions │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ └── matrix-prep │ │ └── params │ │ │ └── params.standard.tcsh │ ├── loops-diff │ │ ├── inputs │ │ ├── code.main │ │ ├── inpdirs │ │ │ ├── loops │ │ │ └── tracks │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ └── submit_step_run.sh │ ├── matrix-distnorm │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ └── params │ │ │ ├── menu │ │ │ ├── params.prep_dist.tcsh │ │ │ └── params.prep_log2-zscore.tcsh │ │ │ └── params.prep_zscore.tcsh │ ├── matrix-filtered │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── filter │ │ │ └── filter-resample │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── params.res_20kb.tcsh │ │ │ ├── params.res_40kb.tcsh │ │ │ └── menu │ │ │ ├── params.res_10kb.tcsh │ │ │ ├── params.res_20kb.tcsh │ │ │ └── params.res_10kb.maxd_10Mb.rotate45.tcsh │ ├── matrix-smooth │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ └── matrix-distnorm │ │ └── params │ │ │ └── params.standard.tcsh │ ├── matrix-stats │ │ ├── inputs │ │ ├── code.main │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ ├── hic-matrix.r │ │ │ └── hic-matrix.so │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ ├── submit_step_run.sh │ │ └── params │ │ │ └── params.standard.tcsh │ ├── submatrix-diff │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ ├── matrix-ic │ │ │ ├── matrix-prep │ │ │ └── matrix-estimated │ │ └── params │ │ │ └── params.s_40kb.tcsh │ ├── virtual4C │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.pipeline │ │ │ ├── code.main │ │ │ └── hicseq-virtual4C.tcsh │ │ ├── inpdirs │ │ │ └── matrix-sparse │ │ └── submit_step_run.sh │ ├── virtual5C │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.pipeline │ │ │ └── code.main │ │ └── inpdirs │ │ │ └── matrix-sparse │ ├── _obsolete │ │ ├── virtual_4c │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── matrix-ic │ │ │ │ └── matrix-prep │ │ │ └── params │ │ │ │ ├── loci.bed │ │ │ │ └── params.scaled.tcsh │ │ ├── bin-filtered │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── filter │ │ │ └── params │ │ │ │ └── params.res_1kb.tcsh │ │ ├── integrate-icgc │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── boundary-strength │ │ │ └── params │ │ │ │ ├── template.tcsh │ │ │ │ ├── params.size_1000kb.tcsh │ │ │ │ ├── params.size_2000kb.tcsh │ │ │ │ ├── params.size_250kb.tcsh │ │ │ │ ├── params.size_5000kb.tcsh │ │ │ │ ├── params.size_500kb.tcsh │ │ │ │ ├── params.size_10000kb.tcsh │ │ │ │ └── generate-param-files │ │ ├── matrix-estimated │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ └── inpdirs │ │ │ │ ├── matrix-ic │ │ │ │ ├── matrix-prep │ │ │ │ └── matrix-hicnorm │ │ ├── matrix-hicnorm │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ └── matrix-filtered │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ ├── matrix-tracks │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ │ ├── matrix-ic │ │ │ │ ├── matrix-diff │ │ │ │ ├── matrix-prep │ │ │ │ ├── matrix-distnorm │ │ │ │ └── matrix-hicnorm │ │ │ └── params │ │ │ │ └── params.standard.tcsh │ │ └── optimal-lambda │ │ │ ├── code │ │ │ ├── inputs │ │ │ ├── clean.tcsh │ │ │ ├── inpdirs │ │ │ └── compare-matrices2 │ │ │ └── params │ │ │ └── params.standard.tcsh │ ├── annotations-stats │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── annotations │ │ └── params │ │ │ └── params.standard.tcsh │ ├── boundary-strength │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── domains │ │ └── params │ │ │ ├── params.k_001.tcsh │ │ │ ├── params.k_002.tcsh │ │ │ ├── params.k_003.tcsh │ │ │ ├── params.k_004.tcsh │ │ │ ├── params.k_005.tcsh │ │ │ ├── params.k_006.tcsh │ │ │ ├── generate-param-files │ │ │ └── template.tcsh │ ├── compare-boundaries │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── domains │ │ ├── submit_step_run.sh │ │ └── params │ │ │ └── params.standard.tcsh │ ├── compare-matrices2 │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── matrix-estimated │ │ └── params │ │ │ └── params.standard.tcsh │ ├── compartments-diff │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ └── compartments │ │ └── params │ │ │ └── params.standard.tcsh │ ├── insulation-diff │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ └── matrix-ic │ │ └── params │ │ │ └── params.standard.tcsh │ ├── matrix-sparse │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ └── hicseq-matrix-sparse.tcsh │ │ ├── inpdirs │ │ │ └── filter │ │ ├── submit_step_run.sh │ │ └── params │ │ │ ├── params.unit_100bp.maxd_5Mb.tcsh │ │ │ └── menu │ │ │ └── params.unit_500bp.maxd_5Mb.tcsh │ ├── translocations │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.pipeline │ │ │ ├── code.main │ │ │ └── scripts-hint-tl.sh │ │ ├── inpdirs │ │ │ └── tracks │ │ └── params │ │ │ └── params.standard.tcsh │ ├── boundary-scores-pca │ │ ├── inputs │ │ ├── code.main │ │ ├── code │ │ │ ├── code.pipeline │ │ │ ├── code.main │ │ │ ├── read-sample-sheet2.tcsh │ │ │ └── hicseq-boundary-scores-pca.tcsh │ │ ├── inpdirs │ │ │ └── boundary-scores │ │ └── submit_step_run.sh │ ├── compare-boundaries-stats │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── compare-boundaries │ │ ├── params │ │ │ └── params.standard.tcsh │ │ └── submit_step_run.sh │ ├── compare-matrices-stats │ │ ├── code │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── inpdirs │ │ │ └── compare-matrices │ │ └── params │ │ │ └── params.standard.tcsh │ ├── compartments-stats │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ ├── code.pipeline │ │ │ └── read-sample-sheet2.tcsh │ │ ├── inpdirs │ │ │ └── compartments │ │ └── submit_step_run.sh │ ├── domains-diff-plots │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ └── domains-diff │ │ └── params │ │ │ └── params.selected-regions.tcsh │ ├── matrix-sparse-diff │ │ ├── inputs │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.main │ │ │ └── code.pipeline │ │ ├── inpdirs │ │ │ └── matrix-sparse │ │ └── submit_step_run.sh │ ├── pygenometracks-plot │ │ ├── inputs │ │ ├── code.main │ │ ├── clean.tcsh │ │ ├── code │ │ │ ├── code.pipeline │ │ │ └── code.main │ │ └── inpdirs │ │ │ └── tracks │ └── index.txt │ ├── __01a-align │ ├── __02a-filter │ ├── __03a-tracks │ ├── __14a-loops │ ├── code.main │ ├── __09a-domains │ ├── code │ ├── __06a-matrix-ic │ ├── __13a-virtual4C │ ├── __14b_loops-diff │ ├── __15a-hicplotter │ ├── data_external │ ├── __02b-filter-stats │ ├── __04a-compartments │ ├── __07a-matrix-stats │ ├── __09b-domains-stats │ ├── __11a-domains-diff │ ├── __12a-matrix-sparse │ ├── __05a-matrix-filtered │ ├── __08a-boundary-scores │ ├── __15b-hicplotter-diff │ ├── __04b-compartments-stats │ ├── __10a-compare-boundaries │ ├── __12b-matrix-sparse-diff │ ├── __08b-boundary-scores-pca │ ├── __10b-compare-boundaries-stats │ ├── submit_main_run.sh │ └── report │ └── report-repo │ ├── nyu_logo.jpeg │ ├── bigpurple_logo.png │ └── exclude_files.txt ├── code ├── code.atacseq-standard ├── code.chipseq-standard │ ├── code.main │ ├── file_backup.sh │ ├── read-sample-sheet.tcsh │ ├── wigToBigWig │ ├── SICER │ │ ├── README.pdf │ │ └── lib │ │ │ ├── BED.pyc │ │ │ ├── UCSC.pyc │ │ │ ├── Utility.pyc │ │ │ ├── GenomeData.pyc │ │ │ ├── SeparateByChrom.pyc │ │ │ ├── make_graph_file.pyc │ │ │ ├── get_total_tag_counts.pyc │ │ │ ├── associate_tags_with_regions.pyc │ │ │ └── Background_island_probscore_statistics.pyc │ ├── clean.tcsh │ ├── obsolete │ │ └── run-qc.sh │ └── clean-all ├── code.hicseq-standard │ ├── code.main │ ├── hicapp │ │ ├── extrasoft │ │ │ ├── hicup │ │ │ │ ├── config_files │ │ │ │ │ └── .conf │ │ │ │ ├── HiCUP_Manual.pdf │ │ │ │ └── HiCUP_Quick_Start.pdf │ │ │ ├── Hi-Corrector │ │ │ │ └── bin │ │ │ │ │ ├── ic │ │ │ │ │ ├── ic_mep │ │ │ │ │ ├── ic_mes │ │ │ │ │ ├── ic_old │ │ │ │ │ ├── split_data │ │ │ │ │ ├── export_norm_data │ │ │ │ │ └── split_data_parallel │ │ │ └── version_track │ │ ├── bin │ │ │ ├── bigWigAverageOverBed │ │ │ └── hicapp_preprocess_hicsum_sort.sh │ │ └── ref │ │ │ └── hg19 │ │ │ └── hg19.genome │ ├── read-sample-sheet.tcsh │ ├── hic-matrix.so │ ├── hicrep_1.0.1.tar.gz │ ├── clean.tcsh │ ├── create-di-matrix.tcsh │ ├── find-active-objects │ ├── find-pending-objects │ ├── calc-matrix-reads.r │ ├── run-fastMeanFilter.tcsh │ └── create-ignored-loci.tcsh ├── code.main │ ├── scripts-submit-jobs │ ├── scripts-save-job-vars │ ├── bedGraphToBigWig │ ├── custom-bashrc │ ├── custom-tcshrc │ ├── pipeline-find-job-ids │ ├── scripts-create-temp │ ├── scripts-qsub-wait-giveok │ ├── scripts-create-path │ ├── obsolete │ │ └── pipeline-execute │ ├── scripts-smartcat │ ├── scripts-send2err │ ├── scripts-sortbed │ ├── scripts-multi-paste │ └── scripts-print-cmdline └── src │ ├── keywords.txt │ └── samtools │ ├── sample.h │ └── errmod.h ├── data └── README.md /pipelines/code: -------------------------------------------------------------------------------- 1 | ../code -------------------------------------------------------------------------------- /pipelines/data: -------------------------------------------------------------------------------- 1 | ../data -------------------------------------------------------------------------------- /pipelines/atacseq-standard/data: 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/pipelines/atacseq-standard/pipeline/matrices/params/params.win_1kb.nbins_1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | set win = 1000 4 | set flank = 0 5 | set nbins = 1 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/matrices/params/params.flank_500nt.nbins_1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | set win = 0 4 | set flank = 500 5 | set nbins = 1 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/matrices/params/params.win_1kb.nbins_1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | set win = 1000 4 | set flank = 0 5 | set nbins = 1 6 | 7 | 8 | 9 | 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More information can be found in the Wiki: 3 | https://github.com/NYU-BFX/hic-bench/wiki 4 | 5 | -------------------------------------------------------------------------------- /code/code.chipseq-standard/SICER/lib/get_total_tag_counts.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.chipseq-standard/SICER/lib/get_total_tag_counts.pyc -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/ic: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/ic -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/matrices/params/params.flank_2500nt.nbins_25.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | set win = 0 4 | set flank = 2500 5 | set nbins = 25 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/matrices/params/params.flank_2500nt.nbins_25.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | set win = 0 4 | set flank = 2500 5 | set nbins = 25 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/align/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter-resample/params/params.reads_100M.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set n_reads = 100000000 6 | 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/loops/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/extrasoft/hicup/HiCUP_Manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.hicseq-standard/hicapp/extrasoft/hicup/HiCUP_Manual.pdf 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--time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hicplotter/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/loops-diff/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-ic/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 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-------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/qc/params/params.default.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload gcc 6 | module load python/2.7 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-scores/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compartments/code/CscoreTool1.1: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter-stats/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hicplotter-diff/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hubs-stats/submit_run-v5c.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=3:00:00 5 | #SBATCH -N 1 6 | 7 | ./run-v5c 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hubs/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set min_cpm = 0.5 6 | set min_dist = 80000 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | 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/pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/template.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 6 | set f = 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-scores-pca/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compare-boundaries/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compartments-stats/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-sparse-diff/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_1000kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 1000000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_2000kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 2000000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_250kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 250000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_5000kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 5000000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_500kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 500000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/cnv/params/params.res_50kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = hint 6 | set resolution = 50 # 50kb resolution 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compare-boundaries-stats/submit_step_run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=48:00:00 5 | #SBATCH -N 1 6 | 7 | ./run 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hubs-stats/submit_run-fithic.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | #SBATCH -J hicbch 3 | #SBATCH --mem=5G 4 | #SBATCH --time=3:00:00 5 | #SBATCH -N 1 6 | 7 | ./run-fithic 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/params.size_10000kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set max_size = 10000000 6 | set f = 0.7 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/virtual_4c/params/params.scaled.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set scale = yes 6 | set loci = params/loci.bed 7 | 8 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/export_norm_data: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/export_norm_data -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/bin-filtered/params/params.res_1kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 1000 6 | set max_dist = 10000000 7 | 8 | -------------------------------------------------------------------------------- /code/code.chipseq-standard/SICER/lib/Background_island_probscore_statistics.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.chipseq-standard/SICER/lib/Background_island_probscore_statistics.pyc -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/split_data_parallel: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NYU-BFX/hic-bench/HEAD/code/code.hicseq-standard/hicapp/extrasoft/Hi-Corrector/bin/split_data_parallel -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/venn-diagram/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | module load r/3.3.0 7 | 8 | set bed_files = "" 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/venn-diagram/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | module load r/3.3.0 7 | 8 | set bed_files = "" 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-cnv/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/optimal-lambda/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set min_improvement = 0.00 6 | set max_pvalue = 0.001 7 | 8 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/clean.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: clean 5 | ## 6 | 7 | if ($#argv != 0) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | rm -rf results 13 | rm -f _tmp* 14 | 15 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/matrix-hicnorm/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-stats/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter/params/menu/params.mapq_20.mindist_5000.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_params = "--mapq 20 --min-dist 5000 --max-offset 500" 6 | 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-ic/params/params.cutoff_0.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set cutoff = 0 7 | 8 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/fastqc/params/params.fastqc.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload jre 6 | module unload java 7 | module load jre/1.8 8 | module load fastqc/0.11.4 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/fastqc/params/params.fastqc.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload jre 6 | module unload java 7 | module load jre/1.8 8 | module load fastqc/0.11.4 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compare-boundaries/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set flank_dist = $bin_size 6 | set black_lists = ($genome_dir/centrotelo.bed) 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/report/report-repo/exclude_files.txt: -------------------------------------------------------------------------------- 1 | .db/** 2 | job* 3 | labels.tsv 4 | *_old* 5 | density_plots/ 6 | hexbin_plots/ 7 | template_intraTAD.tex 8 | loops_unfiltered*.gz 9 | __jdata/ 10 | __jdata_APA/ 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/APA-diff/instructions-run: -------------------------------------------------------------------------------- 1 | #### INSTRUCTIONS #### 2 | 1) populate the ./params/ directory with the .bedpe files of interest (requires the .bedpe extension in the file name) 3 | 4 | 2) RUN step (./run) 5 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_005.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.05" 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_01.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.1" 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_02.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.2" 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/translocations/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = hint 6 | set resolution = 200000 # 200kb resolution 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-prep/params/menu/params.impute.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set prep_params = "--impute" 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-prep/params/menu/params.scale.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set prep_params = "--scale" 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff-plots/params/params.selected-regions.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | # Domains-diff cutoffs 6 | set ddiff_fdr = 0.001 7 | set ddiff_l2fc = 0.4 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-prep/params/params.scale3.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set prep_params = "--scale3 --replace-na" 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.washu.res_40kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = washu 6 | set bin_size = 40000 # this is a commonly used bin size 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/pca/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' 6 | set include_input = 'false' 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | 9 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/pca/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' 6 | set include_input = 'false' 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/insulation-diff/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | # $tool can be "tadsplimer" or "nomikou". 6 | set tool = "tadsplimer" 7 | 8 | set chrom_excluded = 'chr[MY]' 9 | -------------------------------------------------------------------------------- /code/code.main/custom-bashrc: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | export LC_ALL=C 4 | export PATH=$(echo $(echo $PATH | tr ':' '\n' | grep -v '/ifs/home/') | tr ' ' ':') 5 | export PATH=./code/code.main:$PATH 6 | 7 | umask 007 8 | 9 | module load gtools/3.0 10 | 11 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/index.txt: -------------------------------------------------------------------------------- 1 | align 2 | align-stats 3 | 4 | fastqc 5 | qc 6 | 7 | peaks 8 | peaktable 9 | count_peaks 10 | 11 | matrices 12 | 13 | pca 14 | heatmaps 15 | summ-peakanno 16 | venn-diagram 17 | 18 | diffbind 19 | 20 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/index.txt: -------------------------------------------------------------------------------- 1 | align 2 | align-stats 3 | 4 | fastqc 5 | qc 6 | 7 | peaks 8 | peaktable 9 | count_peaks 10 | 11 | matrices 12 | 13 | pca 14 | heatmaps 15 | summ-peakanno 16 | venn-diagram 17 | 18 | diffbind 19 | 20 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_03.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.3" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_05.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.5" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.armatus.gamma_07.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = armatus 6 | set chrom_excluded = 'chr[MY]' 7 | set armatus_params = "-g 0.7" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter/params/menu/params.mapq_15.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set mapq = 15 6 | set mindist = 25000 7 | set filter_params = "--mapq $mapq --min-dist $mindist --max-offset 500" 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter/params/params.mapq_20_mindist0.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set mapq = 20 6 | set mindist = 0 7 | set filter_params = "--mapq $mapq --min-dist $mindist --max-offset 500" 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-prep/params/menu/params.scale_impute45.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set prep_params = "--scale --impute45" 7 | 8 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/project_notes/Project_Notebook.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | author: "" 4 | date: "" 5 | --- 6 | 7 | 8 | 9 | 10 | 11 | --- 12 | # ## ### #### ##### ### ## #### ##### #### 13 | # CONTACT INFO AND CORRESPONDENCE 14 | 15 | --- 16 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/project_notes/Project_Notebook.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | author: "" 4 | date: "" 5 | --- 6 | 7 | 8 | 9 | 10 | 11 | --- 12 | # ## ### #### ##### ### ## #### ##### #### 13 | # CONTACT INFO AND CORRESPONDENCE 14 | 15 | --- 16 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter/params/menu/params.mapq_20.mindist25.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set mapq = 20 6 | set mindist = 25000 7 | set filter_params = "--mapq $mapq --min-dist $mindist --max-offset 500" 8 | 9 | -------------------------------------------------------------------------------- /code/src/keywords.txt: -------------------------------------------------------------------------------- 1 | genomic_ 2 | | cols 3 | | key 4 | | matrix 5 | | matrix2 6 | | mergeuniq 7 | | rows 8 | | table 9 | | vectors 10 | ^genomic_ 11 | ^cols 12 | ^key 13 | ^matrix 14 | ^matrix2 15 | ^mergeuniq 16 | ^rows 17 | ^table 18 | ^vectors 19 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/project_info.txt: -------------------------------------------------------------------------------- 1 | PROJECT-DIR: /project/dir 2 | 3 | PROJECT-ID: Project_ID_ATAC-Seq 4 | 5 | PROJECT-ID-SHORT: ATAC-Seq_ID 6 | 7 | REPORT-AUTHOR: Yixiao Gong 8 | 9 | REPORT-AUTHOR-EMAIL: Yixiao.Gong@nyumc.org 10 | 11 | PI-NAME: Dr. X 12 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/params.topdom.win_5.tcsh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = topdom 6 | set topdompath = "./code/TopDom.R" 7 | set chrom_excluded = 'chr[MY]' 8 | set winsize = 5 9 | 10 | 11 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/create-di-matrix.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: create-di-matrix.tcsh INPUT-MATRIX OUTPUT-MATRIX 5 | ## 6 | 7 | set input = $1 8 | set output = $2 9 | 10 | cat $input | sed '1d' | sed 's/:/ /' | sed 's/-/ /' | tr ' ' ' ' >! $output 11 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/report/notes.tex: -------------------------------------------------------------------------------- 1 | Original location for etoolbox.sty: 2 | $HOME/texmf/tex/tex/latex/etoolbox/etoolbox.sty 3 | 4 | Included this file since older LaTeX installs lacked it 5 | If you have any problems with package conflicts then try removing 6 | this one. 7 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/project_info.txt: -------------------------------------------------------------------------------- 1 | PROJECT-DIR: /project/dir 2 | 3 | PROJECT-ID: Project_ID_ChIP-Seq 4 | 5 | PROJECT-ID-SHORT: ChIP-Seq_ID 6 | 7 | REPORT-AUTHOR: Stephen M. Kelly 8 | 9 | REPORT-AUTHOR-EMAIL: stephen.kelly@nyumc.org 10 | 11 | PI-NAME: Dr. X 12 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/report/notes.tex: -------------------------------------------------------------------------------- 1 | Original location for etoolbox.sty: 2 | $HOME/texmf/tex/tex/latex/etoolbox/etoolbox.sty 3 | 4 | Included this file since older LaTeX installs lacked it 5 | If you have any problems with package conflicts then try removing 6 | this one. 7 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.topdom.win_3.tcsh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = topdom 6 | set topdompath = "./code/TopDom.R" 7 | set chrom_excluded = 'chr[MY]' 8 | set winsize = 3 9 | 10 | 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.topdom.win_7.tcsh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = topdom 6 | set topdompath = "./code/TopDom.R" 7 | set chrom_excluded = 'chr[MY]' 8 | set winsize = 7 9 | 10 | 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/annotations-stats/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set nbest = 50000 # choose top-scoring interactions to calculate enrichments 6 | set score_column = 5 # dist-norm 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-distnorm/params/menu/params.prep_dist.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set preprocess = dist 8 | set distnorm_params = 9 | 10 | 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-smooth/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | set prep = none 7 | set smooth_params = "0,1,2,3,4,5" 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /code/code.main/custom-tcshrc: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source /etc/profile.d/modules.csh 4 | 5 | setenv LC_ALL "C" 6 | set path = `echo $path | tr ' ' '\n' | grep -v '/ifs/home/'` 7 | set path = ( ./code/code.main $path ) 8 | 9 | umask 007 10 | 11 | source inputs/params/params.tcsh 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.topdom.win_5.cpm.common.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = topdom.win_5 6 | set is_normalize = cpm 7 | set use_sample1_ref = FALSE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.topdom.win_5.cpm.ref1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = topdom.win_5 6 | set is_normalize = cpm 7 | set use_sample1_ref = TRUE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/params.hicratio.d_0500.cpm.ref1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = hicratio.d_0500 6 | set is_normalize = cpm 7 | set use_sample1_ref = TRUE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-diff/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set diff_params = "--min-count=50 --min-zscore=2.0 --min-distance=40000" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.hicratio.d_0500.cpm.common.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = hicratio.d_0500 6 | set is_normalize = cpm 7 | set use_sample1_ref = FALSE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-sparse/params/params.unit_100bp.maxd_5Mb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set unit = 100 # maximum sparse matrix resolution (bp) 6 | set maxdist = 5000000 # maximum distance between interacting anchors (bp) 7 | 8 | 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.topdom.win_5.dist_norm.ref1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = topdom.win_5 6 | set is_normalize = dist_norm 7 | set use_sample1_ref = TRUE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/params.hicratio.d_0500.dist_norm.ref1.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = hicratio.d_0500 6 | set is_normalize = dist_norm 7 | set use_sample1_ref = TRUE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/params/params.res_20kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 20000 6 | set max_dist = 0 7 | set ref = $genome_dir/genome.bed 8 | set matrix_params = "--bin-size $bin_size --max-dist $max_dist -R $ref" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/params/params.res_40kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 40000 6 | set max_dist = 0 7 | set ref = $genome_dir/genome.bed 8 | set matrix_params = "--bin-size $bin_size --max-dist $max_dist -R $ref" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.topdom.win_5.dist_norm.common.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = topdom.win_5 6 | set is_normalize = dist_norm 7 | set use_sample1_ref = FALSE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/params/menu/params.res_10kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 10000 6 | set max_dist = 0 7 | set ref = $genome_dir/genome.bed 8 | set matrix_params = "--bin-size $bin_size --max-dist $max_dist -R $ref" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/params/menu/params.res_20kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 20000 6 | set max_dist = 0 7 | set ref = $genome_dir/genome.bed 8 | set matrix_params = "--bin-size $bin_size --max-dist $max_dist -R $ref" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-diff/params/menu/params.hicratio.d_0500.dist_norm.common.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tad_caller = hicratio.d_0500 6 | set is_normalize = dist_norm 7 | set use_sample1_ref = FALSE 8 | 9 | source params/params-template.tcsh 10 | -------------------------------------------------------------------------------- /code/code.chipseq-standard/clean.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: clean 5 | ## 6 | 7 | # shell settings (must be included in all scripts) 8 | source ./code/code.main/custom-tcshrc 9 | 10 | if ($#argv != 0) then 11 | grep '^##' $0 12 | exit 13 | endif 14 | 15 | rm -rf results 16 | rm -f _tmp* 17 | 18 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/peakanno/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | module load r/3.3.0 7 | 8 | set promoter_proximal = 3000 # Extending promoter upstream and downstream by nt 9 | set include_input = 'false' # include ChIP inputs 10 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/bin/hicapp_preprocess_hicsum_sort.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ## 3 | # sort hicsum file based on genomic coordinates 4 | ## 5 | 6 | input=$1 7 | 8 | sed 's/chrX/chr97/; s/chrY/chr98/; s/chrM/chr99/' $input |sort -t $'\t' -k1.4,1.5n -k2,2n -k5.4,5.5n -k6,6n |sed 's/chr97/chrX/; s/chr98/chrY/; s/chr99/chrM/' 9 | 10 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/summ-peakanno/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | module load r/3.3.0 7 | 8 | set promoter_proximal = 3000 # Extending promoter upstream and downstream by nt 9 | set include_input = 'false' # include ChIP inputs 10 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/summ-peakanno/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | module load r/3.3.0 7 | 8 | set promoter_proximal = 3000 # Extending promoter upstream and downstream by nt 9 | set include_input = 'false' # include ChIP inputs 10 | -------------------------------------------------------------------------------- /code/code.main/pipeline-find-job-ids: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: pipeline-find-job-ids RESULTS-DIRS 6 | ## 7 | 8 | set results = "$1" 9 | 10 | set F = `find $results -name 'job*id'` 11 | 12 | set jid = `cat $F | sed 's/.* //'` 13 | 14 | echo $jid 15 | 16 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/peaktable/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set peakdist = 500 # max distances between peaks that will be merged 6 | set annot_params = "annotate2 -i --upstream-dist 100000 --downstream-dist 100000 --proximal-dist 1000 $genome_dir/gene-name.bed" 7 | 8 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/peaktable/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set peakdist = 500 # max distances between peaks that will be merged 6 | set annot_params = "annotate2 -i --upstream-dist 100000 --downstream-dist 100000 --proximal-dist 1000 $genome_dir/gene-name.bed" 7 | 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/align/params/menu/params.bowtie2.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set aligner = bowtie2 6 | set genome = `./code/read-sample-sheet.tcsh $sheet $object genome` 7 | set genome_index = inputs/genomes/$genome/bowtie2.index/genome 8 | set align_params = "--very-sensitive-local --local" 9 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-filtered/params/menu/params.res_10kb.maxd_10Mb.rotate45.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set bin_size = 10000 6 | set max_dist = 10000000 7 | set ref = $genome_dir/genome.bed 8 | set matrix_params = "--bin-size $bin_size --max-dist $max_dist --rotate45 -R $ref" 9 | 10 | -------------------------------------------------------------------------------- /code/code.main/scripts-create-temp: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh -f 2 | 3 | ## 4 | ## USAGE: scripts-create-temp [DIRECTORY] 5 | ## 6 | 7 | if ($#argv > 1) then 8 | usage $0 9 | exit 10 | endif 11 | 12 | set outdir = $1 13 | 14 | if ($outdir == '') then 15 | mktemp _tmp.XXXXXXXX 16 | else 17 | echo $outdir/`cd $outdir; mktemp _tmp.XXXXXXXX` 18 | endif 19 | 20 | -------------------------------------------------------------------------------- /code/code.main/scripts-qsub-wait-giveok: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | #SBATCH -J wait-giveok 4 | #SBATCH --time=0-00:05:00 5 | #SBATCH -p cpu_dev 6 | #SBATCH -n 1 7 | #SBATCH --mem=1G 8 | #SBATCH -o ${1}.out 9 | #SBATCH -e ${1}.err 10 | 11 | source ./code/code.main/custom-tcshrc # customize shell environment 12 | 13 | echo "Done waiting." >! $1 14 | 15 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/align/params/menu/params.gtools.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set aligner = gtools 6 | set genome = `./code/read-sample-sheet.tcsh $sheet $object genome` 7 | set genome_index = inputs/genomes/$genome/bowtie2.index/genome 8 | set align_params = "--min-len 30 --len-diff 5" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains-stats/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MYX]' # excluded chromosomes 6 | 7 | #set group_var = 'cell_type' # grouping variable (from sample sheet) to be used for color assignment) 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/peakanno/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload java 6 | module unload r 7 | module load r/3.3.0 8 | 9 | set promoter_proximal = 3000 # Extending promoter upstream and downstream by nt 10 | set include_input = 'false' # include ChIP inputs 11 | -------------------------------------------------------------------------------- /code/code.main/scripts-create-path: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: scripts-create-path FILE/PATH 6 | ## 7 | 8 | if ($#argv != 1) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set f = $1 14 | 15 | set D = `echo $f | sed 's/\/[^/]\+$//'` 16 | 17 | mkdir -p $D 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /code/code.main/obsolete/pipeline-execute: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: pipeline-execute PROJECT-NAME E-MAIL 6 | ## 7 | 8 | if ($#argv != 2) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set project = $1 14 | set email = $2 15 | 16 | qsub -cwd -m be -M $email -N $project ./run 17 | 18 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/align/params/params.bwa.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module load bwa/0.7.17 6 | 7 | set aligner = bwa 8 | set genome = `./code/read-sample-sheet.tcsh $sheet $object genome` 9 | set genome_index = inputs/data/genomes/$genome/genome/bwa.index/genome.fasta 10 | set align_params = "-A1 -B4 -E50 -L0" 11 | 12 | 13 | -------------------------------------------------------------------------------- /code/code.main/scripts-smartcat: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: smartcat FILES 6 | ## 7 | 8 | if ($#argv == 0) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set F = ($*) 14 | 15 | if (`echo $F[1] | grep -c '\.gz$'` == 0) then 16 | cat $F 17 | else 18 | cat $F | gunzip 19 | endif 20 | 21 | 22 | -------------------------------------------------------------------------------- /code/code.main/scripts-send2err: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: scripts-send2err |INPUT 6 | ## 7 | 8 | if ($#argv == 0) then 9 | set t = `scripts-create-temp` 10 | cat >! $t 11 | sh -c "cat $t 1>&2" 12 | rm -f $t 13 | else 14 | set x = "echo $1 1>&2" 15 | sh -c "$x" 16 | endif 17 | 18 | 19 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/peakdiff/params/params.advanced.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = "easydiff" 6 | set diff_params = "--normalize=normq --scale=log2 --method=mean --fc-cutoff=2.0 --val-cutoff=0" 7 | set annot_params = "annotate2 -i --upstream-dist 100000 --downstream-dist 100000 --proximal-dist 1000 $genome_dir/gene-name.bed" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/peakdiff/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set tool = "easydiff" 6 | set diff_params = "--normalize=none --scale=log2 --method=mean --fc-cutoff=2.0 --val-cutoff=0" 7 | set annot_params = "annotate2 -i --upstream-dist 100000 --downstream-dist 100000 --proximal-dist 1000 $genome_dir/gene-name.bed" 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.h5.res_10kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = h5 # juicer, cool, h5 6 | set resolution = 10000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5) 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.h5.res_20kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = h5 # juicer, cool, h5 6 | set resolution = 20000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5) 8 | -------------------------------------------------------------------------------- /code/code.main/scripts-sortbed: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: sortbed [-i] 6 | ## 7 | 8 | if ($#argv > 1) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | if ($1 == "") then 14 | sort -k1,1 -k6,6 -k2,2n 15 | else if ($1 == "-i") then 16 | sort -k1,1 -k2,2n 17 | else 18 | exit 19 | endif 20 | 21 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/cnv/code/scripts-hint-cnv.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | #SBATCH -J hint-cnv 3 | #SBATCH --mem=10G 4 | #SBATCH --time=12:00:00 5 | #SBATCH -N 1 6 | 7 | module unload python 8 | module load anaconda3/cpu/5.2.0 9 | 10 | conda activate hint 11 | hint cnv -m HICFILE -f juicer --refdir REFDIR -r RESOLUTION -g GENOME -n cnv -o ./hint/cnv/ --bicseq BICSEQ -e ENZYME 12 | conda deactivate 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/interactions/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set loop_params = "--bin-size=$bin_size --lambda-id=1 --min-count=20 --min-zscore=2.0 --min-distance=40000 --max-distance=10000000" # parameters for identifying significant interactions 8 | 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.cool.res_20kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = cool # juicer, cool, h5, homer 6 | set resolution = 20000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5) 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/params.juicer.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = juicer # juicer, cool, h5 6 | set resolution = default # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5) 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-distnorm/params/menu/params.prep_log2-zscore.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set preprocess = log2-zscore 8 | 9 | set max_dist = `echo 10000000/$bin_size | bc` # number of bins (max distance = 10Mb) 10 | set distnorm_params = "--max-dist=$max_dist" 11 | 12 | 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-distnorm/params/params.prep_zscore.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set preprocess = zscore 8 | 9 | set max_dist = `echo 10000000/$bin_size | bc` # number of bins (max distance = 10Mb) 10 | set distnorm_params = "--max-dist=$max_dist --min-score=0" 11 | 12 | 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/matrix-sparse/params/menu/params.unit_500bp.maxd_5Mb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set unit = 500 # maximum sparse matrix resolution (bp) 6 | set maxdist = 5000000 # maximum distance between interacting anchors (bp) 7 | 8 | # NOT IMPLEMENTED YET 9 | #set mindist = 0 # minimum distance between interacting anchors (bp) 10 | 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_001.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=001 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_002.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=002 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_003.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=003 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_004.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=004 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_005.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=005 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/params.k_006.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set filter_centrotelo = true 6 | set bscore_params = prep_none 7 | set flank_boundaries = 20000 8 | set optimal = k=006 9 | set n_categories = 5 # number of boundary categories 10 | set n_boundaries = 0 # number of boundaries per category (0 = auto) 11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.ginteractions.res_10kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = ginteractions # juicer, cool, h5 6 | set resolution = 10000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5 -> GI) 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.ginteractions.res_10kb_raw.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = ginteractions # juicer, cool, h5 6 | set resolution = 10000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5 -> GI) 8 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/find-active-objects: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: find-active-objects RESULTS-DIR 5 | ## 6 | 7 | if ($#argv != 1) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | set R = $1 13 | 14 | set D = `cat $R/.db/db.tsv | skipn 1 | grep -vw missing-inputs | cut -f6` 15 | 16 | foreach d ($D) 17 | if ((! -e $d/job.vars.tsv) && (-e $d/job.err)) then 18 | echo $d 19 | endif 20 | end 21 | 22 | 23 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/tracks/params/menu/params.cool.multires.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set format = cool # juicer, cool, h5 6 | set resolution = 5000,10000,20000,40000 # comma separated list of resolutions, or default (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K) 7 | set keep_all = FALSE # keep intermediate matrices (juicer (hic) -> cool -> h5) 8 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/find-pending-objects: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: find-pending-objects RESULTS-DIR 5 | ## 6 | 7 | if ($#argv != 1) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | set R = $1 13 | 14 | set D = `cat $R/.db/db.tsv | skipn 1 | grep -vw missing-inputs | cut -f6` 15 | 16 | foreach d ($D) 17 | if ((! -e $d/job.vars.tsv) && (-e $d/job.id)) then 18 | echo $d 19 | endif 20 | end 21 | 22 | 23 | -------------------------------------------------------------------------------- /code/code.main/scripts-multi-paste: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: multi_paste FILE1 ... 6 | ## 7 | 8 | if ($#argv == 0) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set prog = `readlink -f $0` 14 | set n = $#argv 15 | set f = $1 16 | 17 | if ($n == 1) then 18 | cat $f 19 | else 20 | shift 21 | $prog $* | join -t ' ' $f - 22 | endif 23 | 24 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/translocations/code/scripts-hint-tl.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -l 2 | #SBATCH -J hint-tl 3 | #SBATCH --mem-per-cpu=20G 4 | #SBATCH --time=12:00:00 5 | #SBATCH -N 1 6 | #SBATCH -c 8 7 | 8 | module unload python 9 | module load anaconda3/cpu/5.2.0 10 | 11 | conda activate hint 12 | hint tl -m HICFILE --refdir REFDIR --backdir BACKDIR --ppath pairix -f juicer -g GENOME -e ENZYME -n tl -p 8 -o ./hint/tl/ 13 | conda deactivate 14 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/diffbind/params/params.norm_edger.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | # module load r/3.2.3 7 | module load r/3.3.0 8 | module unload zlib 9 | 10 | set diffbind_factor = 'group' 11 | set diffbind_blocking_factor = '' 12 | set norm_method = 'EDGER' 13 | set external_table = # additional data (in TSV format) to be merged with diffbind results 14 | 15 | 16 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/diffbind/params/params.norm_edger.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | # module load r/3.2.3 7 | module load r/3.3.0 8 | module unload zlib 9 | 10 | set diffbind_factor = 'group' 11 | set diffbind_blocking_factor = '' 12 | set norm_method = 'EDGER' 13 | set external_table = # additional data (in TSV format) to be merged with diffbind results 14 | 15 | 16 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/diffbind/params/params.norm_deseq2.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | # module load r/3.2.3 7 | module load r/3.3.0 8 | module unload zlib 9 | 10 | set diffbind_factor = 'group' 11 | set diffbind_blocking_factor = '' 12 | set norm_method = 'DESEQ2' 13 | set external_table = # additional data (in TSV format) to be merged with diffbind results 14 | 15 | 16 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/diffbind/params/params.norm_deseq2.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload r 6 | # module load r/3.2.3 7 | module load r/3.3.0 8 | module unload zlib 9 | 10 | set diffbind_factor = 'group' 11 | set diffbind_blocking_factor = '' 12 | set norm_method = 'DESEQ2' 13 | set external_table = # additional data (in TSV format) to be merged with diffbind results 14 | 15 | 16 | -------------------------------------------------------------------------------- /code/code.main/scripts-print-cmdline: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: scripts-print-cmdline PROG ARGV 6 | ## 7 | 8 | if ($#argv < 1) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | foreach a ($argv:q) 14 | if (`echo $a | grep -cE ' |>|<|\(|\)'` == 0) then 15 | echo -n $a 16 | else 17 | echo -n "'$a'" 18 | endif 19 | echo -n ' ' 20 | end 21 | echo '' 22 | 23 | 24 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/generate-param-files: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: generate-param-files NUMBER-OF-BOUNDARIES-PER-CATEGORY 5 | ## 6 | 7 | if ($#argv != 1) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | set n = $1 13 | 14 | foreach k (001 002 003 004 005 006) 15 | set out = params.k_$k.n_$n.tcsh 16 | cat template.tcsh | sed "s//k=$k/" | sed "s//$n/" >! $out 17 | chmod +x $out 18 | end 19 | 20 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-strength/params/template.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | module unload r 5 | module load r/3.3.2 6 | 7 | set filter_centrotelo = true 8 | set bscore_params = prep_none 9 | set flank_boundaries = 20000 10 | set optimal = 11 | set n_categories = 5 # number of boundary categories 12 | set n_boundaries = # number of boundaries per category (0 = auto) 13 | 14 | 15 | 16 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/submatrix-diff/params/params.s_40kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set submatrix_diff_params = ( \ 6 | --pseudo-count=10 \ 7 | --square-size=`echo 400000/$bin_size | bc` \ 8 | --max-dist=`echo 4000000/$bin_size | bc` \ 9 | --logfc-cutoff=0.2 \ 10 | --qval-cutoff=1e-4 \ 11 | ) 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/nucleoatac/params/params.macs_broad.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload gcc 6 | module unload python 7 | # macs now part of python module 8 | # module load macs/2.0.10.20131216 9 | module load python/2.7.3 10 | 11 | set nucleoatac = "" 12 | set nucleoatac_path = '/ifs/home/gongy05/utilities/NucleoATAC/bin/nucleoatac' 13 | set shift_dist = "100" 14 | set genome_fa = $genome_dir/bowtie2.index/genome.fa 15 | -------------------------------------------------------------------------------- /code/src/samtools/sample.h: -------------------------------------------------------------------------------- 1 | #ifndef BAM_SAMPLE_H 2 | #define BAM_SAMPLE_H 3 | 4 | #include "kstring.h" 5 | 6 | typedef struct { 7 | int n, m; 8 | char **smpl; 9 | void *rg2smid, *sm2id; 10 | } bam_sample_t; 11 | 12 | bam_sample_t *bam_smpl_init(void); 13 | int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt); 14 | int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str); 15 | void bam_smpl_destroy(bam_sample_t *sm); 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/heatmaps/params/params.mean.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' # sample sheet column name used to assign group colors 6 | set include_input = 'false' # include ChIP inputs 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | set heatmap_params = "--use-short-names --normalize=mean --log2=true --n-best=4000 --diff=0.75 --nclust=10" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/align/params/params.bowtie2.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set aligner = bowtie2 6 | set genome = `./code/read-sample-sheet.tcsh $sheet $object genome` 7 | set genome_index = inputs/genomes/$genome/bowtie2.index/genome 8 | set align_params = "--local -x $genome_index" 9 | set mapq = 30 10 | set release = inputs/release 11 | set excluding_regions = "~gongy05/references/$genome/blacklist.bed" 12 | set excluding_chrom = "" 13 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/heatmaps/params/params.mean.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' # sample sheet column name used to assign group colors 6 | set include_input = 'false' # include ChIP inputs 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | set heatmap_params = "--use-short-names --normalize=mean --log2=true --n-best=4000 --diff=0.75 --nclust=10" 9 | 10 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/_obsolete/integrate-icgc/params/generate-param-files: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: generate-param-files OVERLAP-VALUE 5 | ## 6 | 7 | if ($#argv != 1) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | set overlap = $1 13 | 14 | foreach size (250 500 1000 2000 5000 10000) 15 | cat template.tcsh | sed "s//${size}000/g" | sed "s//${overlap}/" >! params.size_${size}kb.tcsh 16 | chmod +x params.size_${size}kb.tcsh 17 | end 18 | 19 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/align/code/merge-bam-files.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: merge-bam-files.tcsh R1-BAM R2-BAM GENOME-FA 5 | ## 6 | 7 | if ( ("$1" == "--help") || ($#argv != 3) ) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | set R1 = $1 13 | set R2 = $2 14 | set fa = $3 15 | 16 | samtools view $R1 >! $R1.sam 17 | samtools view $R2 >! $R2.sam 18 | 19 | paste -d'\n' $R1.sam $R2.sam | samtools view -T $fa -b1 - 20 | 21 | rm -f $R1.sam $R2.sam 22 | 23 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/heatmaps/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' # sample sheet column name used to assign group colors 6 | set include_input = 'false' # include ChIP inputs 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | set heatmap_params = "--use-short-names --normalize=none --log2=true --n-best=4000 --diff=0.75 --nclust=10" 9 | 10 | 11 | -------------------------------------------------------------------------------- /pipelines/chipseq-standard/pipeline/heatmaps/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set group = 'group' # sample sheet column name used to assign group colors 6 | set include_input = 'false' # include ChIP inputs 7 | set chrom_excluded = 'chr[MXY]' # excluded chromosomes 8 | set heatmap_params = "--use-short-names --normalize=none --log2=true --n-best=4000 --diff=0.75 --nclust=10" 9 | 10 | 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/annotations/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set genes_bed = $genome_dir/gene.bed # gene BED6 file for annotation of interactions 6 | set cell_type = `echo $objects[1] | cut -d'-' -f1 | cut -d'_' -f1` 7 | if (! -e inputs/data.external/$cell_type) then 8 | set loci_bed = () 9 | else 10 | set loci_bed = `find inputs/data.external/$cell_type -maxdepth 1 -name '*.bed'` 11 | endif 12 | 13 | 14 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compare-matrices/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MYX]' # excluded chromosomes 6 | 7 | set max_dist = `echo 10000000/$bin_size | bc` # number of bins (max distance = 10Mb) 8 | 9 | set compare_params = "--max-dist=$max_dist --n-dist=5 --min-lambda=0.0 --max-lambda=1.0 --n-lambda=6 --gamma=0" # lambda/gamma are only used if estimation was done with max-lambda=Inf 10 | 11 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/calc-matrix-reads.r: -------------------------------------------------------------------------------- 1 | #!/usr/bin/Rscript 2 | #$ -S /usr/bin/Rscript 3 | 4 | ## 5 | ## USAGE: calc-matrix-reads.r MATRIX 6 | ## 7 | 8 | 9 | args <- commandArgs(trailingOnly=T) 10 | if (length(args)==0) { 11 | cat("USAGE: calc-matrix-reads.r MATRIX-1 ...\n") 12 | quit(save="no") 13 | } 14 | 15 | n = 0 16 | for (f in args) { 17 | mat = as.matrix(read.table(f,header=T)) 18 | n = n + sum(mat[upper.tri(mat,diag=TRUE)]) 19 | } 20 | write(n,stdout()) 21 | 22 | quit(save='no') 23 | 24 | 25 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/APA-diff/params/params.res_5kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set APA_resolution = 5000 # set APA resolution 6 | set URm = 2.5 # Upper Right Multiplier: to set the maximum value in the heatmap color scale [ UR = URm * mean(upper right quadrant counts) ] 7 | set fmin_distance = 12 # minimimum distance factor (mdf): mdf * (APA_resolution/sqrt(2)) = minimum distance from diagonal (e.g: mdf=12; res=10000 -> min.distance=84853) 8 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.crane.ins_1000K.tcsh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/tcsh 2 | 3 | set tool = crane 4 | set cranepath = "/ifs/home/cl3011/ROTATION_3/Resources/Software/crane-nature-2015-master/scripts/" 5 | set inssqr = 1000000 # insulation square 6 | set idspan = 200000 # insulation delta span 7 | set insmode = mean # insulation mode 8 | set noise_thr = 0.1 # noise threshold 9 | set bmoerr = 3 # boundary margin of error 10 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 11 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/generate-param-scripts: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | ## 4 | ## USAGE: generate-param-scripts 5 | ## 6 | 7 | if ($#argv != 0) then 8 | grep '^##' $0 9 | exit 10 | endif 11 | 12 | foreach method (inter intra-max) 13 | foreach f (params.hicratio.*.tcsh) 14 | set fnew = `echo $f | sed "s/hicratio/hic$method/"` 15 | echo "$f -----> $fnew" 16 | cat $f | sed "s/^--method=ratio/--method=$method/" >! $fnew 17 | end 18 | end 19 | 20 | chmod +x params.*.tcsh 21 | 22 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/domains/params/menu/params.crane.ins_2000K.tcsh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/tcsh 2 | 3 | set tool = crane 4 | set cranepath = "/ifs/home/cl3011/ROTATION_3/Resources/Software/crane-nature-2015-master/scripts/" 5 | set inssqr = 2000000 # insulation square 6 | set idspan = 200000 # insulation delta span 7 | set insmode = mean # insulation mode 8 | set noise_thr = 0.1 # noise threshold 9 | set bmoerr = 3 # boundary margin of error 10 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 11 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/run-fastMeanFilter.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # shell settings 3 | 4 | ## 5 | ## USAGE: run-fastMeanFilter.tcsh PREP SMOOTH-PARAMS MATRIX-1 OUTPUT 6 | ## 7 | 8 | if ($#argv != 4) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set prep = $1 14 | set smoothing = "$2" 15 | set mat1 = $3 16 | set outdir = $4 17 | 18 | module unload r 19 | module load r/3.3.0 20 | 21 | Rscript ./code/run-fastMeanFilter.r -s $smoothing -p $prep -o $outdir $mat1 22 | 23 | 24 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/APA-diff/params/menu/params.res_10kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set APA_resolution = 10000 # set APA resolution 6 | set URm = 2.5 # Upper Right Multiplier: to set the maximum value in the heatmap color scale [ UR = URm * mean(upper right quadrant counts) ] 7 | set fmin_distance = 12 # minimimum distance factor (mdf): mdf * (APA_resolution/sqrt(2)) = minimum distance from diagonal (e.g: mdf=12; res=10000 -> min.distance=84853) 8 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/peaks/params/params.macs.broad.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module unload gcc 6 | module unload python 7 | # macs now part of python module 8 | # module load macs/2.0.10.20131216 9 | module load python/2.7.3 10 | 11 | set caller_params = "--broad --broad-cutoff 0.1 --format BAMPE --keep-dup all" 12 | set use_input = 'true' 13 | set annot_params = "annotate2 -i --upstream-dist 100000 --downstream-dist 100000 --proximal-dist 1000 $genome_dir/gene-name.bed" 14 | 15 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compare-matrices2/params/params.standard.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MYX]' # excluded chromosomes 6 | 7 | set max_dist = `echo 2500000/$bin_size | bc` # number of bins (max distance = 2.5Mb) 8 | 9 | set compare_params = "--max-dist=$max_dist --n-dist=5 --min-lambda=0.0 --max-lambda=1.0 --n-lambda=6 --gamma=0" # lambda/gamma are only used if estimation was done with max-lambda=Inf 10 | 11 | set prep = none 12 | 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hicplotter-diff/params/params.hicratio-selected-regions.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | module unload python 5 | module load python/gcc/2.7.15 6 | 7 | # TAD caller 8 | set domains_method = hicratio.d_0500 9 | 10 | # Domains-diff method and cutoffs 11 | set domains_diff_method = ${domains_method}.dist_norm.ref1 12 | set ddiff_fdr = 0.001 13 | set ddiff_l2fc = 0.3 14 | 15 | # Run template parameter script 16 | source params/params-template.selected-regions.tcsh 17 | 18 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-scores/params/params.connectivity_2Mb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set boundary_scores_params = ( \ 8 | --min-lambda=0.0 --max-lambda=1.0 --n-lambda=6 --gamma=0 \ 9 | --preprocess=none \ 10 | --distance=`echo 2000000/$bin_size | bc` \ 11 | --distance2=1 \ 12 | --skip-distance=2 \ 13 | --flank-dist=`echo 500000/$bin_size | bc` \ 14 | ) 15 | 16 | 17 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/hicapp/ref/hg19/hg19.genome: -------------------------------------------------------------------------------- 1 | #chrom size 2 | chr1 249250621 3 | chr2 243199373 4 | chr3 198022430 5 | chr4 191154276 6 | chr5 180915260 7 | chr6 171115067 8 | chr7 159138663 9 | chr8 146364022 10 | chr9 141213431 11 | chr10 135534747 12 | chr11 135006516 13 | chr12 133851895 14 | chr13 115169878 15 | chr14 107349540 16 | chr15 102531392 17 | chr16 90354753 18 | chr17 81195210 19 | chr18 78077248 20 | chr19 59128983 21 | chr20 63025520 22 | chr21 48129895 23 | chr22 51304566 24 | chrX 155270560 25 | chrY 59373566 26 | chrM 16571 27 | -------------------------------------------------------------------------------- /pipelines/atacseq-standard/pipeline/align/params/params.bowtie2.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set aligner = bowtie2 6 | set genome = `./code/read-sample-sheet.tcsh $sheet $object genome` 7 | set genome_index = inputs/genomes/$genome/bowtie2.index/genome 8 | set align_params = "--local -x $genome_index --minins 50 --maxins 2000 --no-mixed --no-discordant " 9 | set mapq = 30 10 | set release = inputs/release 11 | set excluding_regions = "~gongy05/references/$genome/blacklist.bed" 12 | set excluding_chrom = "chrM" 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/compartments/params/params.homer.res_100kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | module load homer/4.10 6 | 7 | set tool = homer 8 | set resolution = 100000 # 100kb resolution 9 | set active_mark = FALSE # active mark bed file (e.g. ./params/peaks_ES.bed) 10 | set HK_genes = inputs/genomes/$genome/HK_genes.bed # house-keeping genes bed file 11 | set TSS_genes = inputs/genomes/$genome/gene-tss_annot.bed # TSS bed file 12 | 13 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/hicplotter-diff/params/params.topdom-selected-regions.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | module unload python 5 | module load python/gcc/2.7.15 6 | 7 | # TAD caller and intra-TAD method 8 | set domains_method = topdom.win_5 9 | 10 | # Domains-diff method and cutoffs 11 | set domains_diff_method = ${domains_method}.dist_norm.ref1 12 | set ddiff_fdr = 0.001 13 | set ddiff_l2fc = 0.3 14 | 15 | # Run template parameter script 16 | source params/params-template.selected-regions.tcsh 17 | 18 | -------------------------------------------------------------------------------- /code/code.chipseq-standard/obsolete/run-qc.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | source ./code/code.main/custom-bashrc # setup bash environment 3 | 4 | ## 5 | ## USAGE: run-pca.sh 6 | ## 7 | 8 | # process command-line inputs 9 | if [ $# != 0 ]; then 10 | grep '^##' $0 11 | exit 12 | fi 13 | 14 | # perform PCA 15 | scripts-send2err "=== Performing QC =============" 16 | scripts-create-path results/ 17 | threads=4 18 | scripts-master-loop.sh $threads by-group ./code/chipseq-fingerprint.tcsh results/fingerprint "params/params.*.tcsh" "inpdirs/*/results" 19 | 20 | 21 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/inputs/config-FitHiChIP/configfile: -------------------------------------------------------------------------------- 1 | 2 | Use the configfile_* files 3 | for configuration parameters of different FitHiChIP versions 4 | --------------------- 5 | 6 | configfile_BiasCorrection_CoverageBias 7 | FitHiChIP(L) with coverage bias regression 8 | 9 | configfile_BiasCorrection_ICEBias 10 | FitHiChIP(L) with ICE bias regression 11 | 12 | configfile_P2P_BiasCorrection_CoverageBias 13 | FitHiChIP(S) with coverage bias regression 14 | 15 | configfile_P2P_BiasCorrection_ICEBias 16 | FitHiChIP(S) with ICE bias regression 17 | 18 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/filter/code/peakCall.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #$ -S /bin/sh 3 | #SBATCH -J peakCall_1 4 | #SBATCH --mem=5G 5 | #SBATCH --time=1:00:00 6 | #SBATCH -N 1 7 | 8 | #### RUN EXAMPLE ######## 9 | # ./code/peakCall.sh # 10 | ######################### 11 | 12 | branch=`realpath results/*/*/ | fgrep -v "total"` 13 | n_samples=`ls -l $branch | fgrep -v "total" | wc -l` 14 | make_bam=FALSE 15 | 16 | echo $n_samples 17 | echo $branch 18 | echo $make_bam 19 | 20 | sbatch --array=1-$n_samples ./code/scripts-peakCall.sh ${branch} ${make_bam} 21 | -------------------------------------------------------------------------------- /code/code.hicseq-standard/create-ignored-loci.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | source ./code/code.main/custom-tcshrc # customize shell environment 3 | 4 | ## 5 | ## USAGE: create-ignored-loci.tcsh GENOME-DIR BIN-SIZE 6 | ## 7 | 8 | if ($#argv != 2) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | set genome_dir = $1 14 | set bin_size = $2 15 | 16 | cat $genome_dir/genome.bed | gtools-regions win -s $bin_size -d $bin_size | gtools-overlaps subset -i $genome_dir/centrotelo.bed | gtools-regions shiftp -5p 1 -3p 0 | sed 's/\t/:/' | sed 's/\t/-/' | cut -f1 17 | 18 | 19 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/boundary-scores/params/params.activity_500kb.tcsh: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | 3 | source ./inputs/params/params.tcsh 4 | 5 | set chrom_excluded = 'chr[MY]' # excluded chromosomes 6 | 7 | set boundary_scores_params = ( \ 8 | --min-lambda=0.0 --max-lambda=1.0 --n-lambda=6 --gamma=0 \ 9 | --preprocess=none \ 10 | --distance=`echo 500000/$bin_size | bc` \ 11 | --distance2=`echo 500000/$bin_size | bc` \ 12 | --skip-distance=0 \ 13 | --flank-dist=`echo 500000/$bin_size | bc` \ 14 | ) 15 | 16 | 17 | -------------------------------------------------------------------------------- /code/src/samtools/errmod.h: -------------------------------------------------------------------------------- 1 | #ifndef ERRMOD_H 2 | #define ERRMOD_H 3 | 4 | #include 5 | 6 | struct __errmod_coef_t; 7 | 8 | typedef struct { 9 | double depcorr; 10 | struct __errmod_coef_t *coef; 11 | } errmod_t; 12 | 13 | errmod_t *errmod_init(float depcorr); 14 | void errmod_destroy(errmod_t *em); 15 | 16 | /* 17 | n: number of bases 18 | m: maximum base 19 | bases[i]: qual:6, strand:1, base:4 20 | q[i*m+j]: phred-scaled likelihood of (i,j) 21 | */ 22 | int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); 23 | 24 | #endif 25 | -------------------------------------------------------------------------------- /pipelines/hicseq-standard/pipeline/index.txt: -------------------------------------------------------------------------------- 1 | align 2 | 3 | filter 4 | filter-stats 5 | 6 | tracks 7 | 8 | compartments 9 | compartments-stats 10 | 11 | matrix-filtered 12 | 13 | matrix-ic 14 | 15 | matrix-stats 16 | 17 | #compare-matrices 18 | #compare-matrices-stats 19 | # 20 | boundary-scores 21 | boundary-scores-pca 22 | 23 | domains 24 | domains-stats 25 | 26 | compare-boundaries 27 | compare-boundaries-stats 28 | 29 | domains-diff 30 | 31 | matrix-sparse 32 | matrix-sparse-diff 33 | 34 | virtual4C 35 | 36 | loops 37 | 38 | hicplotter 39 | hicplotter-diff 40 | -------------------------------------------------------------------------------- /code/code.chipseq-standard/clean-all: -------------------------------------------------------------------------------- 1 | #!/bin/tcsh 2 | #$ -S /bin/tcsh 3 | 4 | ## 5 | ## USAGE: run 6 | ## 7 | 8 | if ($#argv != 0) then 9 | grep '^##' $0 10 | exit 11 | endif 12 | 13 | echo '----------------------------------------------------------------' 14 | echo ' ARE YOU SURE YOU WANT TO DELETE ALL RESULTS????' 15 | echo '----------------------------------------------------------------' 16 | echo 17 | echo -n 'Type YES to continue, CONTROL-C TO ABORT...' 18 | set y = $< 19 | if ($y != "YES") exit 20 | 21 | foreach d (__*) 22 | ( cd $d; ./clean.tcsh ) 23 | end 24 | 25 | --------------------------------------------------------------------------------