Illumina stranded RNA-Seq background problem

[NicoBxl]

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 :



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.

[Bukowski]

Well if it's all over the genome, I'd suggest it was genomic DNA. Contamination or sample mix-up.

[Genohub]

Looks like genomic DNA contamination. Did you treat your RNA with DNAse?