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  • How can I estimate overall coverage against a reference database?

    I'm doing de novo assembly on RNA-seq data and I do a stand-alone BLAST against a reference transcriptome. I want to know how much of my assembly aligned, preferably as a percentage so I can estimate quality and have simple statistics to present along with the usual average and median contig lengths-

    Velvet-Oases 6.3%
    Trinity 7.9%

    etc. Is there a tool out there that will estimate how much of a reference database I have covered? Essentially I could add up the lengths of each aligned transcript and divide by the length of all the reference transcripts....not sure if this makes sense, but I could use some advice.

  • #2
    BEDTools has a coverage function. It will tell you how many bases are covered at each depth.

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