Elias Friman

Hi @sergpolly. It's been so long I can hardly remember why I asked for this! But I think it was related to what's happening here: https://github.com/open2c/coolpuppy/blob/c27f509d2474a9fa92217f28b27312ce5ae47c96/coolpuppy/coolpup.py#L1084 and then used in...

Hi @jiangshan529 you must be using an old version, this was changed a long time ago. Try to update with pip or the latest git version.

Hi Noura, I'm not sure how you mean exactly but if you want the distribution of contact scores between regions you can run coolpup.py with --store_stripes which saves individual coordinates...

Hi Noura, You can of course change the --center option and see if that makes a difference and generate stripes to get distributions of values at different resolutions etc. But...

Hi, You are using an old version of the software so it's hard to troubleshoot. Please do a clean install with the latest release and hopefully that will solve it!

Yes that makes sense! I think the main thing for me is that ignore_diags behaviour should be consistent across packages and functions. My intuitive sense would be that None or...

Unfortunately not. The easiest is to generate single pileups for the conditions you want to divide or to extract the matrices individually in python from the data column and divide...

By default coolpup.py uses --nshifts 10, which means that it takes 10 randomly shifted regions as the "expected" background control, which will differ each time. If you want consistent observed/expected...

1. The region in your bed file will be in the center of the pileup, rescaled to a fraction of the total number of pixels. For example, with rescale_flank=1 it...

Your regions are then being filtered out for some reason. Can you try with format="bed", it should do the same the way you've constructed the peak file