calculating the coverage over a gene

[kjaja]

Hi,

I am interested in knowing the mean coverage for a specific region (for example a gene). Is this possible to calculate? If so how ?

Thanks for your help…

[ECO]

From what type of file? This is something you can almost certainly find with just a tiny bit of searching!

[Heisman]

And with the new forum feature you probably saw some threads pop up when you were creating this one that are relevant.

It does depend on your type of file, but you might want to look into GATK DepthOfCoverage.

[azneto]

The questions from ECO are really important in order to answer that.
In anyways, I'm having really good results using Bedtools (http://code.google.com/p/bedtools/).
There's this 'coverageBed' tool that allows one to calculate the coverage of features within a GFF/BED file based on a mapping file (BAM).