Open naturalstay opened 1 year ago
Hi, Thank you for using this script. There are two ways to generate haplotype-resolved Hi-C data.
Thanks, Mengyang
Thank you for your reply.
Now I understand the Hi-C data used here, but I have another question.
The line 107 and line 109 for the HTB.sh
, awk '{if($3==$4) printf("%s\t%s\n",$1,$5+$6);}'
, it seems that only the reads pairs are aligned to the same contig are retained, others were filtered. I think this is unreasonable for Hi-C data. What do you think?
Thanks,
Look forward to your reply.
Thank you for the suggestion. This is a strong constraint on filtering multiple alignments due to the short read length for Hi-C reads. It worked great if the input haplotype-resolved contig assemblies are with good contiguity. But it might reduce links to build scaffolds among contigs. We will remove this constraint in the next version.
Thanks, Mengyang
Thank you for your reply.
Hi, thank you for the powerful script. Now, I have the haplotype-resolved contig-level assemblies, but I don't have the child Hi-C. I have only the Hi-C data of this sample. Can I use this script to get haplotype-resolved Hi-C data. Look forward to your reply.