macs3-project/MACS

Q: multi sample comparison (scATAC)

revolvefire opened this issue · 0 comments

revolvefire commented

Hi @taoliu

Thanks for the wonderful tool!

I've been trying to use the tool (MACS2) for my ATAC data.
I have multiple scATAC samples and I would love to compare there general accessibility.
For example, to see whether different levels of treatment of some sort or a natural developmental process changes the general accessibility of the overall chromosomes.

  1. I've been trying to thoroughly study MACS setup and read through other discussions on the github, but I am still a bit unsure as to what would be the best way to compare these among different samples with different library depth.

  2. What would you recommend as the best output to compare what I wanna compare. (callpeak -> -bdg, bedgraph files?)

  3. Would you consider --SPMR necessary and sufficient for this purpose (comparing multiple samples) or some sort of extra normalization necessary considering how there would be no control data for ATAC-seq and thus --nolambda option used for the callpeak.

Best!