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Old 05-09-2012, 01:40 AM   #1
Location: Guelph, Ontario, Canada

Join Date: Jan 2012
Posts: 31
Default Comparing sets of contigs

Hi, I have no reference genome for my organism, and I have de novo transcriptome contigs (made from 454 and Illumina data assembled with Newbler and Trinity, respectively, then combined with Cap3) for two different tissue types. I'd like to find out how many contigs are unique to each tissue type (that is, do not align at all with the contigs from the other tissue). Is there a tool out there that can do that?
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Old 05-17-2012, 02:39 AM   #2
Location: Raleigh, NC

Join Date: Nov 2008
Posts: 50

A clustering tool like cd-hit should work.
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