Caleb Lareau

Yess sorry; can you send the ls -lrth of the output folder? I just want to verify that all of the files are non-empty > On Jun 13, 2019, at...

Hi, I ave looked over this and I still don’t have a clear recommendation for why this is failing. One option would be to read the bedpe into diffloop and...

Hi @AnaAzambuja, if you want to use Juicebox, then Hichipper isn't necessarily required for this (since it is subsetting the interactions to defined anchors whereas HiC keeps the full contact...

This is a good point. Thanks for catching it. My sense is that it would have little impact if fragments were double counted based on Macs2 duplicate removal, but I...

Hi @armenabnousi, this is a good question, and I think that you're on the right track. The hichipper_qvalue.bdg.tmp indeed serves as input to macs2 bdgpeakcall (see line 116: https://github.com/aryeelab/hichipper/blob/master/hichipper/hicproHelper.py). I...

Thanks for the comment TinTingLi. We’ved push version 0.7.5 (part of a pull request from 0xaf1f) that addresses this. > On Jan 13, 2019, at 3:56 AM, TinTingLi wrote: >...

Seems like a Hi-C Pro issue rather than a hichipper issue? > On Mar 22, 2019, at 9:31 AM, 旖旎 wrote: > > I run HiC-Pro and get too many...

Hi Eduardo, I don’t think that there is an easy way to generate only these. It’s probably easiest to just rerun the tool with the software now installed. > On...

Hi Brandon, I can see why this would be of interest, but it's hard to imagine how to make a statistic that would be applicable here. Every statistic for computing...

So this is an error in the mango FDR calculation. It looks like you only have `6677` PETs in anchors between 5kb and 2Mb, which would suggest that this isn't...