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-   -   Illumina stranded RNA-Seq background problem (http://seqanswers.com/forums/showthread.php?t=31540)

NicoBxl 07-01-2013 05:38 AM

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 :

http://s23.postimg.org/jye2qf3e3/ATL...und_noise3.jpg

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 07-01-2013 11:31 AM

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

Genohub 07-06-2013 08:37 PM

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


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