Adaptor sequences RNA seq -remove?

[sebastion]

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!!

[pmiguel]

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.

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Phillip