Can coolpuppy use raw cool file to perform analysis?

[JiaoLaboratory]

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Hi, thanks for your coolpuppy,

I use "coolpup.py flower_vs_leaf.cool test.bed -p 30 -o out.clpy --rescale --local --ignore_diags 0 --rescale_flank 0.5" to perform my analysis, while I met " ValueError: No column 'bins/weight'found. Use cooler.balance_cooler to calculate balancing weights or set balance=False ";

I want to know how can I set "balance=False", It seems no such option in coolpuppy. Also, in fact I don't want to normolize my hic data, Can coolpuppy use raw cool file to perform analysis? thank you very much!!

[efriman]

Hi,

Yes, using --clr_weight_name "" in the CLI or clr_weight_name=None in the API

https://github.com/open2c/coolpuppy/blob/bba97ac6a2f1a298c617010b5c11531b922cb5c4/coolpuppy/CLI.py#L284

Elias

[JiaoLaboratory]

Yes, great, I have run coolpuppy successfully, and did many alalysises use coolpuppy , It really nice!!! I have a new question, may be out of coolpuppy. In fact I have two hic data, from tissue1 and tissue2. And I want to compare the two data and get a tissue1_vs_tissue2.cool for further analysis. Could you give me some advice on how to generate such file and futher be supported by coolpuppy?

[Phlya]

This is not a typical approach to save a file with difference/ratio etc... It's better to perform the analyses in parallel for both conditions, and then compare the results.

[Phlya]

Glad it now worked well for you!