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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Hichipper on DNase/Mnase type of data (no Resfrag required) #57

Open gundalav opened 6 years ago

gundalav commented 6 years ago

Hi Caleb,

Is there a way to run HICHIPPER on the data that doesn't require ResFRAG? The data such as DNAse/MNase.

I know that HiC-Pro provide such possibility.

Thanks and hope to hear from you again.

G.V.

caleblareau commented 6 years ago

I haven’t done this myself, so I’d recommend some amount of parameter tweaking, but in brief

You’d want to turn off any restriction fragment aware data when calling peaks --skip-background-correction (may be better to call your own outside of hichipper since the background correction won’t be useful)

When processing the loops, you’ll want to use --skip-resfrag-pad

Otherwise, I think that it should be fine? -Caleb

On Oct 16, 2018, at 3:17 AM, gundalav notifications@github.com wrote:

Hi Caleb,

Is there a way to run HICHIPPER on the data that doesn't require ResFRAG? The data such as DNAse/MNase.

I know that HiC-Pro provide such possibility http://nservant.github.io/HiC-Pro/USER_CASES.html.

Thanks and hope to hear from you again.

G.V.

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