Alexandra J. van Rensburg

I get a similar error when running the first and second step in the "Manual curation with juicebox". ./juicer pre $DIR/ST.yash.out.bin $DIR/ST.yash.out_scaffolds_final.agp $DIR/STpurged.fa.fai [E::make_asm_dict_from_agp] sequence ? not found Segmentation fault...

Hi Chenxi, Thanks so much for the quick response! I haven't done any manual editing. The agp was output by yahs. I'm using the contig index file for the original...

Ah, that explains all the problems. Thanks so much. I'll run this tonight and let you know if it's worked. All the best Alex

Dear Chenxi, I've rerun the entire pipeline because I think something went wrong with my initial yahs command. I have managed to work through to the end of "Generate HiC...

It looks like I can't upload the .hic as it's too big. All the best Alex

Dear Chenxi, I can open the .hic file on the web app for juicebox, just not the desktop version. I think I might need the JBAT files to open in...

Hi Chenxi, Changing the juicer_tools to v. 1.9.9 worked! Thank you for all the help! All the best Alex