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Old 10-28-2009, 02:55 PM   #1
amcrisan
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Default MOSAIK on transcriptome data

Has anyone attempted to use the Mosaik aligner on transcriptome data yet? Any thoughts?

Thanks.
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Old 01-27-2010, 02:05 PM   #2
JamesBo
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I have tried it with transcriptome data generated from 454 FLX sequencing. Alignied my reads to the entire "Gene model" dataset for A. thaliana (cDNA with UTRs but excluding introns) - my orgs of interest are within the same lineage. It worked well enough, as far as I can judge - most of the reads excluded were of poor quality, or did not map to a "unique" site. In doing so, I discovered that a large number of sequences were still "contaminated" with primer/adaptor sequence (which I thought had been sufficiently masked or removed). So I am attempting it again . . .
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