shawn

@hardigan Sorry I don't...I did not get any response here and just gave up on it. I guess if you remove or convert the -1 summit values, it will bypass...

Hi Mic, Thanks for your interest! My colleague has made a Galaxy wrapper for PePr, I'll ask her if she will be happy to share the code. Best, Yanxiao

Hi Michal, She says she is still working on it. I'll check with her again later this week. Best, Yanxiao On Mon, Jun 13, 2016 at 1:40 AM, Michał T....

Just an update that she's been busy but is working on adapting the wrapper to the latest version of PePr.

Thanks for letting me know! Yep I think it should be fine. Maybe try updateing the numpy package it might dismiss this warning?

The only way to run PePr without input files is to run in the differential binding mode, where one ChIP file is used as a control for the other ChIP...

Yeah, I think any ChIP-seq input file for the same organism will work (best if it is from the same cell line or tissue).

Definitely. I have started analyzing atac-seq data lately. Will for sure try to adapt it to atacseq and DNase once I understand the characteristics of the data better. On Tue,...

@firatuyulur Yeah you're right. You can do two-condition comparison without "input files". For normalization, the following option will work: `--normalization=inter-group`.

@firatuyulur What is the format of your bed filles? Could you paste the first few lines of it?