xiekunwhy

Hi, Just a bug, haphic pipeline with --correct_nrounds > 0, if there is no contig need to be corrected, corrected_ctgs.txt will not be written, but 04.build step still reading corrected_ctgs.txt...

@ZJ-1992 is this the global heatmap? Would you please show the global (whole genome) heatmap?

also expect an option to output all positions, including those only 0/0 genotype in all sample. thank you @dwpeng , I will try it. Best, Kun

Hi @yangqimeng99 , I was modified a script from endhic (https://github.com/fanagislab/EndHiC), matrix2heatmap.py, it accept HiC-Pro bed and matrix files, not HIC files. If you still have the corresponding bam file,...

Hi Chenxi, Thank you for your reply, and I know the differences now. I need to tell you an other problem. Yahs tend to misjoin and create more butterfly connections...

Hi Chenxi, I use HiC-Pro pipeline to mapping the reads, low quality and multi-mapping has been removed when combining read1 and read2 results. And I got exactly the same results...

@surabhiranavat ，if contig n90 is large enough, try other softwares, like endhic or haphic.

also just want to use gapless to fill gap only.

is there a way to download lineage files manually instead of using compleasm download?

also met the same problem, when snp number is larger than 2 million (or 2 million) , PopGenome may fail to handle. may be you can try https://github.com/panyuwen/Theta_D_H.Est, but the...