A question about Allele.ctg.table

[YuChrming]

Dear Aouthr! For now, allhic is the closest software for success to polyploidy in which I used.But I have a bewilderment. When I use Allele.ctg.table pruning some hi-c signal, anchoring rate is very low. I think if the hi-c signal were filtered too much? So my question is how to achieve selective retention of hi-c signal, or if I can skip this step? PS: What's the function of the first two columns of Allele.ctg.table? Becuase I find the result of haphazard second column not change a bit.

Thanks so much!

[tangerzhang]

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 developed the rescue function, which is able to re-anchor contigs that were missed in previous steps. The first two columns in Allele.ctg.table are meaningless and there is no need to take care of them.