I recently got back reviews for a paper that contained some atac-seq analysis. The paper followed a standard analysis pipeline where peak calling was done using macs followed by differential analysis between two samples using deseq2.
One of the reviewers mentioned that we should include 'an analysis accounting for Tn5 cleavage bias' and that this can be done 'by analyzing nucelosome positioning at different locations in the genome'. Now I am a little confused by what this actually means.
I have found nucleosome calling pipelines like nucleoatac and hmmratac and can make nucleosome positioning plots but I am not sure how that relates to Tn5 bias. I was wondering if anyone here has any ideas on what kind of analysis can be done illustrate the absence of tn5 bias?