Cut&Tag / ChIPseq analysis
Hi Biostars community, I have a beginner question on how to analysis Cut&Tag / ChIPseq data. We use IgG control as the background when doing peak calling using SEACR (https://github.com/FredHutch/SEACR). What to do if we have multiple IgG control (biological replicates)? Do you merge IgG control replicates (merge bam files) before calling peaks? Thank you!
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Unless you have a peak caller that explicitely can accept replicates summing them up (merging) is probably the only option. For ChIP-seq I am only aware of PePr which can take replicates but it is not so widely used afaik.
Thank you for your comment! I tried merging IgG control bam files and this way I have much more reads in the control bam (4 times more). Would this create a problem?