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  • Inquiry: minimum length of reads for referece-based assembly or de novo assembly

    Hi all,

    While doing QC preprocessing of RNA-seq reads, what could be the minumum length of reads for a reliable assembly: reference-base or de novo assembly?

    I am a greenhand in RNA-seq area, and just wonder, when we met bad quality data, to what extent could we trim the reads?

    for example, as fastqc results shown in the attachment.
    Do I have to trim the first 10bps and the last 20bps?
    Is 50bps left enough for (tophat->cufflinks) assembly?

    Thank you very much in advance!!!!!!
    Attached Files

  • #2
    Did you get a new insight on this problem? I posted a similar question here:

    http://seqanswers.com/forums/showthr...919#post117919

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