Hello everyone !!
I've started to work on ATAC-seq data and I would like to know how to process data after peak calling ?
I've two group to study, patients and healthy control, and after performing peak calling to see regions of open chromatin (that correspond to genes potentially expressed), I would like to look for the notably differences between the 2 groups in order to see what's wrong with patients. For instance, I would like to see where some genes are expressed in patients and not in control and vice versa.
Is there a simple way to do those analyses ? Or maybe mutiple ways ? maybe is there a similar analyse from an other NGS technique like ChIP-seq, MNase-seq, DNase-seq, etc... ? What are the tools or pipeline usually used for that ?
Thank you in advance !!