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c-zhou / yahs

Yet another Hi-C scaffolding tool
MIT License
123 stars 18 forks source link

Sex chromosomes #49

Open acdarby opened 1 year ago

acdarby commented 1 year ago

I have tired running a few data sets through were we have XY linkage groups represented well in the contigs but they fail to scaffold with YAHS - The autosomes look nice but the sex chromosomes do not! This is not unexpected as the Ys can be very challenging but the problems with the X maybe suggest I am missing a trick!! Are there any special parameters I should use when working with genomic data from the heterogametic sex (in this case XY)?

c-zhou commented 1 year ago

Hello @acdarby,

YaHS expects a single-haplotype assembly. The pseudoautosomal regions might cause the mess between XY chromosomes. Unfortunately, we do not really have any tricks for solving this currently. My only suggestion is to extract the XY contigs and scaffold them separately.

Best, Chenxi