WACS

[aawdeh]

Incorporating controls is an essential step in ChIP-seq analysis. The controls are used to account for the background signal, while the remainder of the ChIP-seq signal captures true binding or histone modification. However, a recurrent issue is the existence of different biases in different ChIP-seq experiments. Depending on which controls are used, different aspects of ChIP-seq bias are better or worse accounted for. As a result, peak calling can generate different peaks for the same ChIP-seq experiment. This extension allows for weighted or "smart" controls to model the non-signal effect for a specific ChIP-seq experiment. It first generates the weights per control to model the background distribution per ChIP-seq experiment and is then followed by peak calling.

https://www.biorxiv.org/content/10.1101/582650v1

[taoliu]

Thanks! I will review this!

[taoliu]

@aawdeh If we plan to merge the new feature of WACS into MACS, could we just add the "-w" or "--control-weights" option to the regular "callpeak" function, instead of creating an almost identical "callpeak_wacs" command? PS: I am specifically discussing merging WACS as a new feature in MACS in this PR page. Also, should I hold this PR until your paper is published in a peer-reviewed journal?

[aawdeh]

@aawdeh If we plan to merge the new feature of WACS into MACS, could we just add the "-w" or "--control-weights" option to the regular "callpeak" function, instead of creating an almost identical "callpeak_wacs" command? PS: I am specifically discussing merging WACS as a new feature in MACS in this PR page. Also, should I hold this PR until your paper is published in a peer-reviewed journal?

@taoliu Thank you for your reply! Yes, that works. Also, I think it should be fine going ahead with this PR. We already have the paper on bioRxiv and will be submitting it soon to a peer-reviewed journal.