Mapping an assembled genome to a sex chromosome

Question

[Lilnet]

Hi,

I would like to find out if there is a method to determine which scaffold were successfully mapped to the reference. In my case I am mapping an assembled reference genome A (scaffolds) to the sex chromosomes (ZW) from another reference genome B (chromosomal assembly).

My aim is to determine which of the scaffolds in reference genome A mapped successfully to the sex chromosome from reference genome B.

Would appreciate any advice!

Cheers

Answer 1

[Xyson]

Hello, Did you find a way to do this? If yes, please let me know how you did it.

Thanks!