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  • MOSAIK on transcriptome data

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

    Thanks.

  • #2
    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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