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  • Adaptor sequences RNA seq -remove?

    Hi all,

    This is probably a really dumb question but I was just wondering if someone could explain to me how adaptor sequences affect RNA seq data.
    I've carried out some sequence alignments on my samples without trimming or removing them & the majority of reads(over 85%) are aligning....is this normal? would it improve if I removed them or do I need to?

    Thanks in advance for advice!!

  • #2
    Depends on the mapping engine. A few (Novalign, MAPQ and SOAP, and Bioscope, I think) will effectively do the clipping for you.

    Also, if your inserts are mostly longer than your sequence reads, you may have little adapter sequence in your data set.

    --
    Phillip

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