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  • IonTom
    Member
    • Apr 2014
    • 32
    #1

    Trimming RNAseq data

    When looking at our data the first 10 to 12 bases look strange i FASTQC both for baseq qaulity and composition. This is well known for RNAseq data.

    The question now is should I just trim them and the last 3 bases or leave it as it is. Because there seems to be a bias but i think aligner like STAR or subjunc can deal with it.

    Also does TopHat2 do soft clipping, and could this cause a problem.

    Many thanks.
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      Leave the first bases intact if this is RNAseq data. That should not cause any problems with mapping.

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