mRNAseq and SNPs call, how can we make this as good as possible?

[sindrle]

Hi! I have worked some time on a mRNAseq set, single-end. Its a high quality set and lots of biological replicates (200+).

My question is, how could I best contribute to the methodology used for SNPs call in mRNAseq? What do we need tested to improve this method?

- See more at: http://gatkforums.broadinstitute.org....TKwxqyLk.dpuf

[dpryan]

One nice thing to do with such a large dataset is to look for common sites of RNA editing that might not have already been found. One of the steps in calling SNPs from RNAseq is removing such sites, but I don't know how good the databases of these really are (though I suspect these are human samples, so the data is probably already at least semi-OK there). Depending on the make-up of your samples, perhaps they could be used to help in that.

[sindrle]

Very good, Ill look into that!

I have 48 samples now and getting 150 more i december.

This is not the main project, but I guess it could be set to good use for other things as well. So I want to be prepared.

[lre1234]

Out of curiosity, is there a database of RNA-editing sites? Sort of a dbSNP but for RNA-editing.