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Old 03-25-2010, 06:32 AM   #23
Location: Montreal

Join Date: Oct 2009
Posts: 63

Sure, the only disadvantage of transcriptomics if uniformity. Since some will be more expressed than others and the fact that this is tissue/time specific will biase the finding of snps for specific transcripts.

If you know that what you are looking for is in an moderately to highly expressed transcript this is a great and cheap way of getting the answer.

If all you know is that it's expressed but don't know in which tissue or if it's highly expressed or not, reduced genome approach targeting exons might be better...if you know the genome, which I guess, is not your case.

Abyss does a good job at assembling RNA, I don't know about velvet. There are special considerations when assembling RNA because alternate splice sites confuses assemblers if they don't know they're there.
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