Why do I find the sequencing primer sequence in my data?

[soev]

Hi all,

I am sequencing small RNAs on a GAIIx Illumina platform. I prepared my small RNA seq library by adding 5' and 3' Illumina compatible adaptors and subsequent reverse transcription and PCR. The Illumina sequencing primer should bind to the 5' adaptor and the first nucleotide read should correspond to the 5' end of my original RNA molecule. However, in my data I still find a lot of sequences corresponding to the 5' adaptor/sequencing primer. Does anyone know how this is possible?

thanks!

Soetkin.

[gringer]

What constitutes 'a lot'? We've got about 0.5% of our sequences in a SOLiD4 run that map to the PCR primers. We suspect these are due to primer dimers that were present in the sample.

[soev]

About 2,5 % ... it seems quit a lot ... but it could be the primers ... Thanks for helping!