hichipper into .hic file

[AnaAzambuja]

Hi, I am using hichipper and diffloop to analyse my H3K27Ac HiChip data. Is that a way to convert hichipper output into .hic file for JuiceBox visualization?

Thanks, Ana

[caleblareau]

Hi @AnaAzambuja, if you want to use Juicebox, then Hichipper isn't necessarily required for this (since it is subsetting the interactions to defined anchors whereas HiC keeps the full contact matrix). I'd recommend converting the HiC-Pro output directly into .hic files via the hicpro2juicebox.sh shell script available rom the HiC-Pro authors: https://github.com/nservant/HiC-Pro/blob/master/doc/UTILS.md