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.gitignore
.gitignore
 
 
ATACdemultiplex
ATACdemultiplex
 
 
README.md
README.md
 
 
atac_plotTSSenrich.py
atac_plotTSSenrich.py
 
 
bdgTobw.sh
bdgTobw.sh
 
 
bedToBdgBw.sh
bedToBdgBw.sh
 
 
binned_count_bam.sh
binned_count_bam.sh
 
 
cal_peak_overlap_mat.R
cal_peak_overlap_mat.R
 
 
callAME_fisher.sh
callAME_fisher.sh
 
 
convert_name.sh
convert_name.sh
 
 
correctDup.py
correctDup.py
 
 
correctDup.sh
correctDup.sh
 
 
correctLibQC.R
correctLibQC.R
 
 
correctLibQC_from_rmChrM.R
correctLibQC_from_rmChrM.R
 
 
download_igm.pbs
download_igm.pbs
 
 
download_igm.sh
download_igm.sh
 
 
fastqSpliter.py
fastqSpliter.py
 
 
filter_chr.sh
filter_chr.sh
 
 
makeNameDic.py
makeNameDic.py
 
 
mutliCoreTarFolder.sh
mutliCoreTarFolder.sh
 
 
parseAME.sh
parseAME.sh
 
 
plotCoverage.sh
plotCoverage.sh
 
 
plotQC.R
plotQC.R
 
 
plot_peak_overlap_mat.R
plot_peak_overlap_mat.R
 
 
qc_bam.sh
qc_bam.sh
 
 
rename_use_file.sh
rename_use_file.sh
 
 
results_transfer.sh
results_transfer.sh
 
 
results_transfer_dev.sh
results_transfer_dev.sh
 
 
rmChrM.sh
rmChrM.sh
 
 
run10xCellRanger.pbs
run10xCellRanger.pbs
 
 
run10xCellRanger.sh
run10xCellRanger.sh
 
 
run10xPipeline.pbs
run10xPipeline.pbs
 
 
runBcl2fastq.pbs
runBcl2fastq.pbs
 
 
runBulkCHIP_fastq.pbs
runBulkCHIP_fastq.pbs
 
 
runDemux10xATAC.pbs
runDemux10xATAC.pbs
 
 
runDemux10xATAC_RNA.pbs
runDemux10xATAC_RNA.pbs
 
 
runDemux10xRNA.pbs
runDemux10xRNA.pbs
 
 
runDemux10xRNA.sh
runDemux10xRNA.sh
 
 
runDemuxSnATAC.pbs
runDemuxSnATAC.pbs
 
 
runFastQC.sh
runFastQC.sh
 
 
runFastQC_2.sh
runFastQC_2.sh
 
 
runFastQC_2trim.pbs
runFastQC_2trim.pbs
 
 
runFastQC_2trim.sh
runFastQC_2trim.sh
 
 
runFastQC_bz2.pbs
runFastQC_bz2.pbs
 
 
runFastQC_bz2.sh
runFastQC_bz2.sh
 
 
runGEM.sh
runGEM.sh
 
 
runPipeline_TA.pbs
runPipeline_TA.pbs
 
 
runPipeline_snATAC.pbs
runPipeline_snATAC.pbs
 
 
runPipeline_snATAC_fastq.pbs
runPipeline_snATAC_fastq.pbs
 
 
runSetQC.pbs
runSetQC.pbs
 
 
run_bcl2fastq_custom.pbs
run_bcl2fastq_custom.pbs
 
 
share_files.sh
share_files.sh
 
 
simplify_name.sh
simplify_name.sh
 
 
snATAC_barcode_comp_v2.txt
snATAC_barcode_comp_v2.txt
 
 
split_between.sh
split_between.sh
 
 
split_gt.sh
split_gt.sh
 
 
split_lt.sh
split_lt.sh
 
 
tagToBdg.sh
tagToBdg.sh
 
 
tagToBwScale.sh
tagToBwScale.sh
 
 
tagToFragBed.sh
tagToFragBed.sh
 
 
tagTobw.sh
tagTobw.sh
 
 
tree
tree
 
 

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utility_epigen

The shell utility @ epigen tscc.

  • correctLibQC.R: correct the libQC report txt after rm ChrM from final bam. It need rm temp bams from output folder.
  • plotCoverage.sh: plot heatmap of coverage from bigwig file over tss or bed regions using deeptools

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