run epic without control samples

biocore-ntnu / epic

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER

http://bioepic.readthedocs.io

MIT License

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run epic without control samples #77

Closed james-chuang closed 6 years ago

james-chuang commented 6 years ago

Hello,

I'm interested in trying epic on some ChIP-exo and ChIP-nexus datasets. Unlike traditional ChIP-seq, these protocols don't generate an input library, which is a problem since epic requires control libraries to be specified in order to run.

Is it possible to make the control samples optional? Section 2.1.5 of the 2009 SICER paper is about using a random background model in the absence of a control library.

endrebak commented 6 years ago

Perhaps https://github.com/dariober/SICERpy does what you want? Or MACS2? I have no plans of adding support for ChIP only as I do not have the time and do not need it myself, unfortunately.

I gain nothing for having made epic publically available and can't really spend much time on it except for the stuff that I need. Sorry!

james-chuang commented 6 years ago

No worries!

The option is available using SICER itself, so between that and SICERpy I'll be able to get what I need. Just thought I'd ask since epic looked like the most user-friendly/maintained project of the three.