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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Is it possible that *.a_ctg.gfa represents sex chromosome? #318

Open Jung19911124 opened 1 year ago

Jung19911124 commented 1 year ago

Hi,

I ran Hifiasm on Hifi reads derived from an inbred strain of XX/XY species. In order to determine Y chromosome sequences, I extracted genomic DNA from male.

The result file, *.p_ctg.gfa, included some fragments, which are not found in reference assembly derived from female (XX individual). Those fragments must be linked to Y chromosome, but total length of the fragments was much smaller than I expected.

Then I realized *.a_ctg.gfa also consists of the small fragments which are not found in the female genome, and have a reasonable length for Y chromosome.

Is it possible that *.a_ctg.gfa represents heterogametic sex chromosome when we used an inbred strain?

Any advice would be appreciated. Best,

Jung

chhylp123 commented 1 year ago

Yes, it is possible and it also depends on how large the Y chromosome is.

Jung19911124 commented 1 year ago

Dear chhylp123,

Thank you for the reply. My species is an insect, so chromosome size is relatively small. Y chromosome of this species is estimated to be < 40 Mbp.