How to use XYalign

[vunguyen1907]

Hi. Let me describe my data to see if I can use XYalign to find Y-contigs

My data is whole genome re-sequencing data with coverage of ~ 15X, including male and female fish (around 20 each sex)
I have reference genome assembly (~ 1Gb) but unfortunately not sex determined yet as the sample fish was small.

I also have transcriptomic data of 6 males/females.

Can you advise if the data can be used XYalign to find the Y chromosome?

Thanks
Vu

[thw17]

Hi Vu,

Unfortunately, XYalign can't yet identify Y (or W) chromosome haplotypes in resequencing data if a contig/scaffold isn't in the reference assembly.

Best,
Tim