Hello everyone, I have ChIP-Seq datasets. With Bowtie2, now I have BAM files. I mostly use SeqMonk for these kind of analyses but I do not think it does not have a tool for differential ChIP-Seq analysis. I used MACS for peak calling (on SeqMonk) and I have values too.
1) Anyone knows a suitable and fast (Windows 10 would be awesome) tool for this analysis?
2) Does a basic statistical analysis (like t-test) to the log2 peak values of each sample work?
3) Do DESeq2 or EdgeR to the raw counts work?