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popgenDK / SATC

Sex assignment through coverage
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RNA-seq data #4

Open d00bin opened 2 years ago

d00bin commented 2 years ago

Hello!

Is it possible to use SATC with RNA-seq data?

aalbrechtsen commented 2 years ago

Probably not however we have not tried it.
However, to my (very limited) understanding XX individuals do not have higher expression from their Xchromosome compared to XYs X chromosome because one of them is deactivated. And since SATC uses depth-of-coverage to identify the sex chromosome then it will probably not work. however, If you already have indexed bam files then you can quickly test it.