What’s the answer? (sex of pigs) (no, seriously)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This question I highlight this week has made me giggle for several reasons–but it is a serious issue for researchers. One of reason it is funny is just how little we actually get out of the sequence still–some people think we should have everything solved with some sequence data now–yet clearly even this presumably obvious genetic trait is not always so straightforward.  The other thing is I’d bet any hog farmer could give you this answer in about a millisecond just by looking at an animal. (I’m sure there’s a cartoon in there somewhere….) The other thing is that my first thought would be to call the person who gave the sample to ask for some details about the sample. You’d think that would be important metadata you’d ask for in a handoff of the samples….?

This week’s question:

How to know sex of a pig by viewing bamfiles

Hello, I have bamfiles from some genes on the x-chromosomes for some individual animals but the sexes of the animals are not known. Is there a way I can determine the sexes by looking at read coverage in the bamfiles or by any other means? Thanks


At first the question didn’t specify the species–which is key to the ultimate answer. But it did reveal other issues about the quality of the pig genome assembly at this point, but even other genomes as well.  Check out the discussion. I thought it was interesting.