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  • SEQquestions
    replied
    Is anyone willing/able to give an overview of the % of reads they get aligning to miRbase for fresh/FFPE miRNAseq?

    Leave a comment:


  • SEQquestions
    started a topic Quick poll: miRNAseq alignment stats

    Quick poll: miRNAseq alignment stats

    Hi,

    I'm hoping to get an idea of average alignment stats for miRNAseq (human only). Please could anyone working in this area reply with an overview of their experiments (type of tissue/RNA extracted/library prep kit/sequencer) and the rough % of total reads and/or those passing QC that align to a) miRbase precursors and/or b) the human genome. NB looking for read stats not unique sequence stats (i.e. counting collapsed reads by the number of times they are observed)

    As an example, in our work:

    Total RNA used in NEB Next small RNA prep kit and sequenced on HiSeq2000. QC is removal of adapters and then removal of reads <13bp.

    Cell lines: 87% (+/= 9%) of reads pass QC and, of those, 33% (+/- 15%) align to miRbase precursors.

    FFPE: 80% (+/- 10%) of reads pass QC. Of those, 3% (+/- 1%) align to miRbase precursors and a further 65% (+/- 5%) align elsewhere in the human genome.

    It would be interesting to see how this compares

    Cheers

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