Hi-C linkages between non allelic contigs in pruning step

[mentorlg]

Hi tangerzhang,

I have a question about pruning step.

In pruning step, ALLHiC removes Hi-C linkages like...

1. Hi-C linkages between allelic contigs using allelic contig table
2. Hi-C linkages between collapsed region and other contigs by retaining only strongest Hi-C signal

then, how can be removed Hi-C linkages between non-allelic contigs ..?

Looking forward to an answer Best Regards

Amelia

[tangerzhang]

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 non-allelic contigs from the bam files.

[mentorlg]

Hi tangerzhang,

Do you mean that in pruning step, ALLHiC removes Hi-C linkages in three ways as listed in below...?

1. Hi-C linkages between allelic contigs using allelic contig table
2. Hi-C linkages between collapsed region and other contigs by retaining only strongest Hi-C signal
3. Hi-C linkages between non-allelic contigs (remove based on the bam files)

[tangerzhang]

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 linkages between collapsed region and other contigs by retaining only strongest Hi-C signal

[mentorlg]

If then, Hi-C linkages between non-allelic contigs removed before pruning step..???

[tangerzhang]

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

[mentorlg]

If I have a high-quality Hi-C mapping, is there no Hi-C links between non-allelic contigs ..?