problem with Running on already aligned files

aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

http://aidenlab.org

MIT License

402 stars 180 forks source link

problem with Running on already aligned files #273

Open mycecilia opened 2 years ago

mycecilia commented 2 years ago

The -S chimeric option is not available anymore with the latest version of juicer. When I tried to use the -S merge to run on already aligned HiC bam file following the instructions on the Usage page, it gave me the error:

(-: Looking for fastq files...fastq files exist sort: cannot read: '/home/juicer/splits/*.sort.txt': No such file or directory ***! Some problems occurred somewhere in creating sorted align files.

Could you please look into this? Thank you.

Shiyu

sa501428 commented 2 years ago

Hey @mycecilia, We will look into this. In the meantime, I would suggest using Juicer 1.6 from https://github.com/aidenlab/juicer/releases

zoomlion commented 2 years ago

Maybe you could follow this protocol instruction: Rick Masonbrink's intruction