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aryeelab / hichipper

A preprocessing and QC pipeline for HiChIP data
MIT License
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Hichipper with HiCUP input #29

Open rdali opened 6 years ago

rdali commented 6 years ago

Hello Caleb,

We are interested in running hichipper on our HiChIP data. However, your pipelines (Hi-C, capture HiC and HiChIP) are based on HiCUP which results in a bam that contains all the Valid reads. Is it possible to use hichipper with HiCUP? If you can think of a quick fix then I can help edit the code for our internal version to include hichipper in our institute's workflow.

Thanks! Rola

caleblareau commented 6 years ago

Hi Rola,

Yes, I've been meaning to expand-- this seems straightforward enough.

Could you possibly provide a sample .bam file of say chromosome 22 (human) OR chromosome 19 (mouse) from HiCUP that I could test this on? I'll also work on fixing up the enhancement that was noted on the previous issue. Thanks!

rdali commented 6 years ago

Hello Caleb,

I have a downsampled example with 2 million reads from human public data if that works. I cant seem to be able to attach it anywhere ("format not supported" it says); can I send it by email?

caleblareau commented 6 years ago

Sure thing-- caleblareau@g.harvard.edu