Tanger Zhang

Hi @linshengnan09 I apologize for the misleading. The ```Allele.gene.table``` are not the same with ```Allele.ctg.table```, and we have avoided to use ```Allele.gene.table``` in our next release. And I also modified...

[Prune.tar.gz](https://github.com/tangerzhang/ALLHiC/files/6698301/Prune.tar.gz) Hi @linshengnan09 , yes.It is normal. The prune step may take some time and space when the bam file is big. However, during the development of ALLHiC2, we have...

@linshengnan09 BTW, are you working on a simple diploid genome or a complex polyploid genome that needs haplotype-resolved assembly? If it is a simple diploid genome, such as rice and...

Actually, the heterozygous ratio is only 0.36% and you do not need a phased assembly. In other words, prune will be not helpful. Would you like try a wrapped script...

Sure, not problem. My email address is: [email protected]

> Hi the links are broken. I have the same issue, it filled my file system and the system ran out of space due to the huge log file. This...

Did you mean you will use the output of purge_haplotigs as a reference genome? If so, the purge_haplotigs generates primary contigs and these data can be used to construct a...

The large group is mostly caused by chimeric assembly errors in contigs. You can firstly use ALLHiC_corrector to correct the chimeric contigs and then link them using ALLHiC scaffolding. The...

Hi @theshowmustgolangon You can use dotplot and Hi-C heatmap to assess the quality of Hi-C scaffolding.

Dear @YuChrming I also noticed that the pruning function filters some Hi-C signals that may be useful to link non-allelic contigs, resulting in a low anchoring rate. That's why we...