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Old 07-15-2015, 04:12 AM   #3
NGS_New_User
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Location: USA

Join Date: Sep 2012
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Hi Linnea,

Thanks for the suggestion and the article links. This should be extremely helpful, I am grateful! I had thought of the 'crap reads' in ChrY but I wasn't sure yet of how to handle them. I will try your suggestion and compare the two.

I am currently trying to get the ChrX using the same approach that you have suggested. However since we have quite a fragmented assembly (~200k contigs) I am getting a lot of contigs with varying M:F ratio of between ~0.45-0.55. Our closest related species would be Musca domestica but since it is not yet completely annotated, I guess I can try using the ChrX from Drosophila melanogaster.

Thanks!
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