Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice)
I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:
- Adapter and T-overhang trimming with Cutadapt
- Mapping to reference genome with bowtie2
- PCR duplicate removal (Picard), quality and blacklist filtering (sambamba or samtools)
- Peak calling with MACS3
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 of the following modes?
- 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!