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Old 07-14-2015, 11:20 PM   #2
Location: Uppsala, Sweden

Join Date: Mar 2010
Posts: 23


For the ChrY I would actually suggest that you assemble the male reads instead, then map the female reads and define the ones with zero female read coverage as Y scaffolds. Doing the other way around, you would surely get the Y reads but also any contamination or "crap"-reads from the sequencing.

We tried both of above in a non-model organism (bird) and it worked much better with the assembly-first approach. (Our paper is here:

The method is partly taken from here: Hall, A. B. et al. Insights into the preservation of the homomorphic sex-determining chromosome of Aedes aegypti from the discovery of a male-biased gene tightly linked to the M-locus. Genome Biol. Evol. 6, 179–191 (2014).
And they have a script here:

To get the ChrX is trickier, but one thing you can try is to map both female reads and male reads to the female assembly and compare the coverage quota (of course normalized if you have different amounts of female and male data). All chromosomes should in theory have similar (normalized) male and female coverage except for the X-chromosome, where the M:F ratio should be 0.5. Because of sequencing bias of course not all scaffolds will have the same coverage, so it's probably best to use this method in combination with some other method, like blasting the scaffolds to a related species with a defined X-chromosome. For our organism it worked well when coverage was very high (>100X).

Good luck!
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