Multi-mapping issue

[mgy19]

Hello
When I use bowtie2 -a or -k for multiple map, HIC Pro does not work properly as you said.How can I modify mergesam to work properly?

[YichaoOU]

Sorry I don't have the exact solution because it will take some time.

For my virus insertion project, I know where the insert is, so I can check if R1 or R2 mapped to this insert. If so, generate the possible cis-pairs (For example, virus is inserted in chr1,chr2, and R1 mapped to the insert in chr1 but R2 mapped to chr2, so the pair should all be in chr2 where R1 is the chr2 insert). If not, this is just multi-map reads in the regular genome, we should just let it go.

Do you have similar case where you have a custom genome? If you just deal with a regular genome, you can just ignore multi mapping.