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  • 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.

  • #2
    Leave the first bases intact if this is RNAseq data. That should not cause any problems with mapping.

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