Question: how to identify a sequencing sample's gender
0
gravatar for 897598644
3.8 years ago by
89759864480
China
89759864480 wrote:

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!

sequencing next-gen genome • 4.1k views
ADD COMMENTlink modified 3.8 years ago by Pierre Lindenbaum109k • written 3.8 years ago by 89759864480
3

Just being pedantic, but you can't.  You can likely determine sex, but not gender.

ADD REPLYlink written 3.8 years ago by swbarnes23.8k
1

the answer does depend on the sex-determination system for the organism

ADD REPLYlink written 3.8 years ago by Istvan Albert ♦♦ 77k

Other than asking them (they don't usually like it when you try to manually check)?

ADD REPLYlink written 3.8 years ago by Devon Ryan81k

thx for your promt answer.

the questionaire did not show the answer

ADD REPLYlink written 3.8 years ago by 89759864480

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).
 

ADD REPLYlink written 3.8 years ago by Devon Ryan81k

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 :)

ADD REPLYlink written 3.8 years ago by Daniel Swan13k
2
gravatar for Pierre Lindenbaum
3.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum109k wrote:

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).

ADD COMMENTlink written 3.8 years ago by Pierre Lindenbaum109k

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.

Many thx.

ADD REPLYlink written 3.8 years ago by 89759864480
1

ask a new question.

ADD REPLYlink written 3.8 years ago by Pierre Lindenbaum109k

You mean i put a new post?

ADD REPLYlink written 3.8 years ago by 89759864480

Is that for RNA seq and/or Exom-Seq?

ADD REPLYlink written 3.3 years ago by ido.sloma20

DNA sequencing in general. For RNAseq, samples will cluster strongly by gender (I've used that fact to determine mouse gender after the fact).

ADD REPLYlink written 3.3 years ago by Devon Ryan81k

Ever come across a Klinefelter?

ADD REPLYlink written 3.0 years ago by Aaron Statham1.1k

Yep, I found XIST expression in a male sample and later on found markers on the X chromosome for which the individual was heterozygous.

ADD REPLYlink written 14 months ago by WouterDeCoster30k

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

 

thanks

ADD REPLYlink written 2.8 years ago by paumarc0

">> 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

ADD REPLYlink written 2.8 years ago by swbarnes23.8k
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