excuse me: could you tell me how to identify a sequencing sample's gender?
Being a greenhand, i would appreciate if you give me detailed procedures.
Thx in advance!
Just being pedantic, but you can't. You can likely determine sex, but not gender.
the answer does depend on the sex-determination system for the organism
Other than asking them (they don't usually like it when you try to manually check)?
thx for your promt answer.
the questionaire did not show the answer
You can always align to a genome with both X and Y chromosomes and then determine this based on relative Y chromosome coverage. I've done a similar thing with mouse RNAseq datasets (people have an unfortunate habit of not noting the genders and not controlling for them tanks the results) with 100% accuracy (so far at least).
Counting het genotype calls on the X chromosome is also a pretty good discriminator as there aren't so many in an XY individual as an XX one :)
In our lab, we run GATK DepthOfCoverage with 3 beds (autosomes, chrX, chrY) to get 3 mean corverages. Females should have cov(X)>>cov(Y).
thx for your reply.
There was another question always bothering me and this is the link C: How to find de novo mutation in trio sequencing data in perl or python script? .
I was wondering how you finish this kind of work in your lab.
ask a new question.
You mean i put a new post?
Is that for RNA seq and/or Exom-Seq?
DNA sequencing in general. For RNAseq, samples will cluster strongly by gender (I've used that fact to determine mouse gender after the fact).
Ever come across a Klinefelter?
Yep, I found XIST expression in a male sample and later on found markers on the X chromosome for which the individual was heterozygous.
can you explain what does means cov(x)>>cov(y)? I suppose that cov stands for coverage, but could you give some code and/or numbers as example
">> means "greater than. ">>" means a lot greater than, like 100x higher, so much higher that the smaller thing is mathematically insignificant. A woman should have nearly z coverage on the Y chromosome
When array genoptyping older populations using blood, there is a known loss of Y in older males (and smokers) and XO mosaicism in older females (but not an actual Turner's diagnosis). In your experience is this still seen in sequencing?
Put an alternate way, does this method ever result in cov(X)>>cov(Y) and little-to-no X heterozygosity?