PCRPpipeline

Bioinformatic pipeline used to process PCRP datasets

Pipeline requirements

• python 2.7.14
• python - matplotlib
• Java 8 or later
• perl v5.10.1 or later
• bedtools v2.27.1 or later
• samtools 1.7
• MEME v5+
• ChExMix v0.45 available here: https://github.com/seqcode/chexmix
• • Compiled JAR should be moved here: /QC-pipeline/external_app/

Command to run pipeline:

sh 11_RUN_MEP_QC_XO.sh -s sampleID.txt -a /path/to/QC-pipeline

sampleID.txt file format

4-column tab-delimited file containing the information required to run the pipeline for each sample

SampleID	Full path to SAMPLE.bam	Full path to CONTROL.bam	Full path to Reference features

Reference features folder structure

• REF/Genome
• • REF/Genome/hg19.fa
• • REF/Genome/hg19.fa.fai
• • REF/Genome/hg19.info
• • REF/Genome/hg19_background_model.txt
• REF/Blacklist
• • REF/Blacklist/hg19_Blacklist.bed
• REF/TSS
• • REF/TSS/hg19_TSS_2000bp.bed
• REF/CTCF
• • REF/CTCF/hg19_CTCF_2000bp.bed
• REF/Motif_Coord/
• • REF/Motif_Coord/JASPAR2020_CORE_vertebrates_non-redundant_pfms_meme.txt
• • REF/Motif_Coord/hg19_JASPAR2020_cluster_occurrence.tab
• • REF/Motif_Coord/JASPAR2020_cluster_ID.out
• • REF/Motif_Coord/hg19_JASPAR2020_MotifCluster.gff.gz
• • REF/Motif_Coord/TOMTOM_Fail.png
• • REF/Motif_Coord/NoMotifDetected.png
• • REF/Motif_Coord/JASPAR2020_weblogo/JASPAR_cluster_*.png
• REF/ChromatinState
• • REF/ChromatinState/chromHMM/chromHMM.bed.gz
• • REF/ChromatinState/segway/segway.bed.gz
• • REF/ChromatinState/Repeat/hg19_RepeatMasker.bed.gz