HiChIP vs HiC input?

[Mlad22]

Hi

I have a more general question about the method here and hope that you can you give me an advise.

I would like to know if this method works well if I input a global HiC dataset (not HiChIP) together with transcription factor or histone ChIPseq data. Would it still call the right loops? Could you tell me if you would recommend this or not and why?

Thanks for your help!

Best,
Mladen

[Mlad22]

hello?

[caleblareau]

Hi, apologies for the delay. The tool will still be useful to aggregate abundances of PETs between two or more histone peaks (I've used this functionality myself quite often). However, the counts are typically very low for Hi-C data and it does not give particularly valid loop calls, which makes things challenging to interpret. There may still be value in processing your samples with hichipper though.