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Old 05-03-2012, 02:37 PM   #5
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

indeed. do you think that one would have to engage in a massive pairwise BLAST session between assemblies in order to match them up?

Maybe, for that reason, it would be easiest to pool all reads into a massive FASTQ and run them through ABySS at once to get a master list of transcripts and then perform quantification through other means.
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