search

vaquerizaslab / fanc

FAN-C: Framework for the ANalysis of C-like data
GNU General Public License v3.0
107 stars 14 forks source link

hic files format after the fanc auto pipeline #184

Closed Knetsy closed 8 months ago

Knetsy commented 8 months ago

Hello,

I have successfully run fanc auto on my fastq files and I got indeed .hic files. I would like to use the plotgardener R package to plot Hi-C data but I got an error that says "Hi-C magic string is missing, does not appear to be a hic file." Could you please indicate me how to have proper .hic files? I tried the fanc subset command to extract contacts from a specific chromosome and then try to load this .hic files using the plotgardener R package and I got the same error.

Thank you.

Best,

Deborah

kaukrise commented 8 months ago

Juicer and FAN-C just happen to use the same file extension. FAN-C output is not compatible with tools that expect a Juicer .hic format. You can either try to convert to a Juicer file using fanc to-juicer on the .pairs file from FAN-C, or directly use a Juicer preprocessing pipeline.