I have ATACseq data from one WT sample and one KO sample, and want to find different peaks between them. Can I just use MACS2 -t -c for this purpose?
MACS2 callpeak -t ATACseq_KOsample -c ATACseq_WT_sample -f BED -n "$prefix" -g $genome -p $pval_thresh --shift $shiftsize --extsize $smooth_window --nomodel -B --SPMR
According to the tutorial of MACS2, it firstly calculates λ from ChIPseq IP, then tests input against Possion distribution based on λ. The p-value generated is used for peaks detecting.
Do you think the same logic can be used for the comparison between two ATACseq samples? in my case, a WT mice and a KO mice.
Thanks a lot!
To clarify, I don't have replicates for WT/KO so far, which is a problem, but I will have them.