Pipeline for ChIP-Seq Analysis at the Harada Lab
Programs required:
-macs2 (Version)
-bedtools (Version)
-idr (Version)
-perl (Version)
-python (Version)
-phantompeakqualtools (Version)
For simplification purposes, it is important that all bam files (ChIP and Inputs) to be present in the same folder as the script.
General Usage:
perl chipseq_pipeline_v4_032119 chipseq.br1.dedup.bam chipseq.br2.dedup.bam input.br1.dedup.bam input.br2.dedup.bam