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Old 07-01-2013, 05:38 AM   #1
NicoBxl
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Location: Belgium

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Default 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 :



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.
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Old 07-01-2013, 11:31 AM   #2
Bukowski
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Well if it's all over the genome, I'd suggest it was genomic DNA. Contamination or sample mix-up.
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Old 07-06-2013, 08:37 PM   #3
Genohub
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Looks like genomic DNA contamination. Did you treat your RNA with DNAse?
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