dudcha

Hi MiaoShi, You can ignore these: these are warnings in case you have contigs with unusual names. (I should at some point get rid of them.) Thanks, Olga > On...

This looks like a library with very uneven coverage distribution. This causes default misjoin correction to misfire and flag everything with high cov as problematic. Load 1d tracks to help...

Hi huanfa, This is not an error but a warning, should not cause you issues. Usually this might happen if you are running several jobs to build Hi-C maps on...

Can you share the .out and .err? > On Jul 15, 2019, at 9:54 AM, huanfa wrote: > > @dudcha > Thanks for your reply. I have solved the problem...

Hi huanfa, This does not seem to contain the error stream, so can't use this to diagnose. One thing that may cause problems on this stage is bash version: note...

Hello yilunhuangyue, You might consider polishing in Juicebox Assembly Tools. I would suggest looking through the Genome Assembly Cookbook for instructions, as well as other possible solutions. The Cookbook is...

Hello wj1106, Are you running in diploid or haploid mode? Diploid does not preserve total sequenced bases count. If you are in haploid, what are you counting, the total length...

Hi ncgrijsmiao, Usually we recommend editing the .rawchrom.assembly file: this is the one most typically used with Juicebox Assembly Tools, and the scripts for generating the fasta based on that...

Hello Saurabh, 1. the script you are pointing to is not relevant in this case. The rainbow track is created from the chrom-length assembly to draft. Make sure you are...

Saurabh, Chromosome-length assembly in this script is assumed to be a continuous gradient from 0 to 1 (for the first -c scaffolds). The relevant column says how the draft assembly...