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differential binding analysis of cut-tag peak data

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

chip-seq
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updated by rpolicastro rpolicastro • written by 17318598206 • 17318598206

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

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written by rpolicastro rpolicastro

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.

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written by jared.andrews07 jared.andrews07

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