Does anyone have a protocol or recommended pipeline for doing differential peak/binding analysis in Partek. I want to compare ATAC-seq results from two different conditions, but a ChIP-seq based pipeline would also be useful.
Diffbind and csaw seem good but these are not available in Partek. EdgeR and DEseq2 are available, but to use these I would need some way to turn MACS2 called peaks into features before I can use them. Any advice please?
Thank you very much!