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  • featureCounts

    Hi all,

    I am using (for the first time) featureCounts to get gene level counts in a RNAseq experiment... It is mouse RNAseq and polyA RNA were extracted...

    A quick look at the results shows up to 15% of reads which are unassigned because of no overlap with any feature.

    Do you normally have the same stats?

    s.

  • #2
    I just checked one dataset (mouse liver), where ~5% had no feature, ~3% were ambiguously mapped (a non-stranded protocol), and ~19% were not uniquely mapped. ~75% were counted if we exclude unmapped reads. This is similar in a mouse hippocampus dataset that I just checked. Obviously if you include unmapped reads then these percentages would go down a bit.

    So, that unassigned percentage seems a bit high, but perhaps there's a good biological reason for that (e.g., in tumors or sperm).

    Comment


    • #3
      Post #29. Response from Wei Shi (author of featureCounts): http://seqanswers.com/forums/showthr...t=49506&page=2

      Comment


      • #4
        Hi dpryan,

        I already removed the non uniquely mapped so yes, it's a bit lower if we consider all the mapped reads... and yes, it's sperm...

        So I should not worry :9

        Thanks a lot

        Comment


        • #5
          Yeah, sperm will inherently be different, since you have depletion of mRNAs. My sperm datasets aren't polyA enriched, they're ribo-depleted, so I don't have any numbers for comparison.

          Comment

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