Hi All

I've just been trying to analyse some ATAC-Seq data and have got a little stuck. I'm relatively new to bioinformatics and ATAC seems like a bit of a step up from RNASeq analysis!

My data are ATAC-Seq reads from 6 samples from 2 conditions - 3 replicates / condition. I've been following the Galaxy training tutorial for ATAC-Seq (https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html) and have done the peak calling on all my samples with MACS2.

However, the tutorial essentially stops here and doesn't go into any way of comparing peaks between samples, so I was wondering what the best way to do this is? Clearly I need to produce a file detailing a common set of peaks between samples and then a count matrix with the number of reads which fall within these peaks for each sample, which I could then analyse using eg. DESeq2. However, I'm not super familiar with MACS2 or its outputs so not sure what's the best approach.

Can anyone recommend a good way of going about this?

Thanks!