Q: MACS2 snATAC

[AnjaliC4]

Hi, thanks for this truly awesome tool. As you may already know, there is a lot of discussion around using which parameters for MACS2 peak calling in single-nucleus ATAC-seq. I have been using -q 0.01 -g hs --nomodel --nolambda --extsize 200 --shift -100 -f BED the above parameters to for my PE100 snATAC. I wanted to confirm with you if this makes sense from how MACS2 works and what will be the implication of these parameters. My understanding is that -f BED will allow peak calling on both the reads, then --nomodel will disable poisson modelling and shit the window for peak calling to 100 bp 3' and then extend it to 100 bp both sides. Please let me know if I understand this correctly and if this makes sense to you. Do you think that rare peaks from rare cell populations may still be missed with these parameters? Thank you.

Anjali