Hello biostars community !!
I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data in the case of no replicate in samples ?
I've performed Macs2 for peak calling and used IDR (irreproducible discovery rate) and intersectBed on my first set of ATAC-seq data (which contains replicates) to have peaks in common between my samples but I've a second set of data without replicates and I would like to do the same analyse...
Is there a way to do the same thing on my second set where I have no replicates ? What are the tools I've to use to do that ?
Then, I would like to make differential expression on my two sets of datas. Is the strategy the same in the 2 cases (with replicates and without replicate) ? What strategy do you use for differential expression in ATAC-seq data ?
Thank you in advance !!