[wgs-assembler-users] Find all pairs that cross a gap

[Ole K. T. <o.k...@ib...>]

Hi,
I've been thinking a bit. In some of the assemblies I have, half the gaps
are of size 20. This means that the contigs that are on each side of the
gap, was supposed to overlap, but had too much differences to be able to be
merged (10%). Have I understood this correctly?

Is half the gaps in size 20 an expected number?

I'm wondering if these failed overlaps is because of heterozygosity, for
example, the wrong haplotype is tested for overlap. Could this be the case?
I'm not sure how to test this though.

One possibility is that there's a difference in the length of the
haplotypes. So if I can find all the insert sizes of the pairs that span a
gap of 20 bases, I might see that they group into two different groups. If
the length differences is large, this should be pretty clear. Is there a
way to get all the insert sizes of the pairs that map across these gaps?

Thank you.

Ole