Calling differential peaks on ATAC-seq data
My lab has recently run an ATAC-seq analysis on 3 biological conditions (Day 0, day 1 and day 7) with two replicates assigned to each. Once the data is finally generated, I will need to use some differential peak calling software to identify regions of differential accessibility between the 3 conditions. So far, I’ve thought that MACS2 would be the best option for this (The bdgdiff tool), but after reading around, THOR seems like it may be easier to use and provide better results.
Can anyone give me some advice about the potential benefits or limitations of using these two programs with ATAC-seq data?
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