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  • Ohrfandl
    Junior Member
    • Jul 2013
    • 1
    #1

    How can I check the quality of my assembly (e.g. compared to RefSeq)?

    I have assembled a mouse transcriptome using cufflinks and I was wondering how I can check the quality of the assembly? I would like to compare it to an existing annotation (e.g. RefSeq) and ask two things:

    1. How many RefSeq transcripts could I assemble completely?

    2. Which RPKM cutoff should I use? Therefore, I would like to group all assembled genes according to their RPKM (log10 intervals) and ask how many percent of transcripts in each group are completely assembled when compared to RefSeq.

    Is there such a tool available?

    Thanks in advance!
    Tags: assembly, cufflinks, rnaseq, transcriptome
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