Mapping an assembled genome to a sex chromosome
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!
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