macs3-project/MACS

Use of IDR after running MACS3 for ATAC-seq data

OrangeyO2 opened this issue · 2 comments

OrangeyO2 commented

Use case
I am analyzing ATAC-seq data from human cells. I am planning to performed the following as part of my pipeline:

  1. Adapter and T-overhang trimming with Cutadapt
  2. Mapping to reference genome with bowtie2
  3. PCR duplicate removal (Picard), quality and blacklist filtering (sambamba or samtools)
  4. Peak calling with MACS3

Describe the problem
Looking at online pipelines, the use of IDR post peak calling with MACS2 seems to be recommended.
Is this still the case with the recently released MACS3 v3.0.0 when used with either the
default: macs3 callpeak -f BAMPE -t ATAC.bam -g hs -n test -B -q 0.01, or
hmmratac: macs3 hmmratac

Also, when IDR is used, MACS2 seems to be run with p-value cutoff of 0.1. If the use of IDR is still recommended post MACS3, should it be run with -p 0.1 as well?

Thanks in advance for your help!

taoliu commented

@OrangeyO2 Yes. You can still follow the pipeline for MACS2 -- using p-value cutoff 0.1 in callpeak command for IDR. The basic function of callpeak has minimum changes between MACS2 and MACS3.

OrangeyO2 commented

@taoliu Thank you!