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  • 75% reads mapped, but 40% map to 'no feature'

    Hi,

    I have mRNA sequencing data, from low amount of cells using SMARTer kit and Illumina GA, 36 single end reads.

    I mapped them with gsnap to mouse mm10 genome and got count table with HTSeq. 75% of reads mapped to genome, but only 35% mapped to exons, while as much as 40% to 'no feature'.

    Before I was analysing similar data, also obtained from little amount of cells with SMARTer kit (but 75bp PE reads) and I was 85% reads mapped, while only 10% mapped to 'no feature'.

    Did anyone experience that? Where should I look for problems? Could it be DNA contamination of the sample? Or maybe problem lies somewhere in mapping?

    my commands were:
    gsnap -A sam -B 5 -t 10 -n 1 -Q --nofails –D /path/path/mouse -d mouse -s mouse sample.fq > sample.sam

    htseq-count sample.sam /path/path/Mus_musculus.GRCm38.70.gtf > sample.txt

    Thanks

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