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Old 07-14-2015, 10:35 AM   #1
Location: USA

Join Date: Sep 2012
Posts: 41
Question Extracting sex chromosomes from sequenced genomic DNA reads or assembled genome

Hi everyone.

I have two sets of data; male and female (Illumina sequenced, PE reads, ~300 million each, 100bp) of a non-model organism (insect). Since it has no reference genome I performed a de novo assembly on both sexes.

I would like to extract the sex chromosomes from each sex.
For the Y chromosome, I mapped all the male reads to the female draft genome and the unmapped reads that remained I grouped them as the 'Chr Y' reads. I then performed an assembly of the unmapped reads to get the 'ChrY' contigs. Does this sound like a reasonable way to tackle this?

I am a little stranded on how to get the 'Chr X' reads. Does anyone have any idea of how I can do this, or any suggestions? It will be highly appreciated.
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