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  • Velvet/Oases transcript expression level?

    Hi,
    I am in the process of de novo transcriptome assembly from a non-model eukaryote. I have 17 million 65 bp, paired-end reads that I have assembled with Velvet and then Oases. This gives nice results in that I am getting full-length contigs that appear reasonable when compared to orthologues in related model eukaryotes. However, I am really after relative transcript expression levels. Does anyone know if there as a way that I can get information on that from this software combination?

  • #2
    Hi Simon,

    I'm not by any means an expert on this, but you probably have two options:

    1. Convert the kmer coverage in the stats.txt file to base-coverage and use that as a proxy for expression level

    2. Align the reads to the assembled transcripts using something like Bowtie and then extract the coverage of each transcript using SAMTools

    Hope that helps!

    Comment


    • #3
      Velvet question

      How can one extract all of the reads that were used in the assembly, in order to do the re-mapping step you described?

      Comment


      • #4
        Under the contrib/extractContigReads directory in Velvet you'll find a script to do this

        Comment

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