differential binding analysis of cut-tag peak data

Question

[17318598206]

I have cut-tag data of protein A in three kinds of cells (only one duplicate), I would like to know the difference of binding sites of this protein in these three kinds of cells, and how to analyze them. I have the BAM file after comparison and the peaks file after MACS2

Answer 1

[rpolicastro]

You can use software such as DiffBind to find differential peaks. Refer to their documentation for more information.

[jared.andrews07]

Note that DiffBind (and pretty much any other method of doing this, e.g. csaw) requires replicates. You should try to get replicates for your conditions. The only single-sample comparison method I know of is MAnorm, though I'd urge you to view any results from it with a healthy dose of skepticism.

edit: MAnorm2 has apparently been released, so maybe try that version.