Tanger Zhang

Hi @ardy20 The error was caused by the typo of MBOI name. Your input is MOBI. Alternatively, you can simply the restriction sites: GATC. We have not tested Omni-C libraries....

> Dear Sirs, > is there any planned support for OmniC data in allHiC? > thanks Hi @diriano I have not had a chance to test OmniC data. Could anyone...

Hi @diriano That would be great if you could share with me the contig assembly and OmniC reads. My gmail is tanger.zhang@gmail and google drive works for me. Thanks!

Hi Amelia, Below are my responses: **1. What is the difference between collapsed regions and chimeric contigs in pruning step?** _In polyploid genomes, some of the homologous regions (i.e., allelic...

Hi Amelia, Please see my responses below: First, I want to assemble autopolyploid genomes, not monoploid. In number 2, I understand that I have to use contigs twice of the...

Hi Amelia, A dot-plot analysis between your target genome and a reference genome (could be either a close relative or a monoploid assembly) will help you to determine which chromosomes...

Hi Amelia, Sorry that I missed this message. Hi-C linkages were calculated based on read pairs that span two contigs, and therefore you can remove these paired-end reads derived from...

Hi @mentorlg ALLHiC prune removes only the 1) and 2) HiC links, rather than reads between non-allelic contigs. 1). Hi-C linkages between allelic contigs using allelic contig table 2). Hi-C...

Not quite sure why do you need to remove Hi-C links between non-allelic contigs? Are they low-quality mapping?

Hi @linshengnan09 It seems that the contig name are inconsistent between Allele table and input.fasta. Would you please indicate us how did you generate the allele table? I would recommend...