Inner mate distance of paired-end reads counted in the coverage in IGV

Question

[mari.felix5723]

Hello everyone !

I am wondering if the Interactive Genome Viewer (IGV) display the inner mate distance of paired-end reads in the coverage.

Thank you very much !

[Istvan Albert]

It is not clear what you are asking. Are you asking whether a region bridged over a pair will be reported as covered (coverage increased by 1) even though none of the sequences of the pair covers that region?

[mari.felix5723]

That is exactly what I am asking.

Answer 1

[mari.felix5723]

I think I found my answer.

I used Bedtools genomecov to extract the coverage and it was the same as in IGV. Then I used the -pc option of genomecov (calculates coverage of intervals from left point of a pair reads to the right point) and the coverage was increased. Therefore, I think that IGV doesn't include the bases of the inner mate distance in the coverage.

Can someone is able to confirm this please ?

Thanks.

[bluskale]

Based on manually counting reads in IGV, it seems that coverage in IGV strictly displays the coverage of the reads and nothing more, with no consideration for the underlaying fragment of paired end sequencing data (particularly evident with viewing reads as pairs). Not only does the insert region get dropped from the coverage calculations, but overlapping pair mates are also double counted in the overlap region.

Due to splicing etc, accurate quantification of the fragment coverage is probably rather difficult with eukaryotes. With prokaryotes however, this should be possible. I was hoping that bamCoverage of the deepTools package would accomplish this, but it also seems to have some issues.