This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Illumina Stranded Rna-Seq Background Problem

Hi everybody,

We perform RNA-Seq experiments using illumina TruSeq total RNA stranded (with RiboZero) and we have strange results compared to previous samples. We sequenced on a HiSeq2000 2x100bp.

Here a picture of the alignment results :

enter image description here

The two first lane are a previously sequenced sample (same kit) and the two below are a new one. You can see that on the new ones, there is a background. And it is almost on the whole genome like that...

Someone has an idea of ​​where the problem comes from?

Thanks a lot,

N.

illumina rna-seq
• 3,209 views • link
written by Nicolas Rosewick Nicolas Rosewick

Maybe contamination with genomic DNA?

• 212 views • link
written by Michael Dondrup Michael Dondrup

That was my first thought too..

• 0 views • link
written by User 59 User 59

Ok thanks. Is there a way to have like a "contamination value" estimation (like a value between 0 and 1 giving the intensity of DNA contamination - 0 is no contamination and 1 full contamination (so reads everywhere on both strands) ) ?

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

0 answers

No answers yet.

Log in to answer this question.

More posts like this