Illumina Stranded Rna-Seq Background Problem

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10.8 years ago

Nicolas Rosewick 10k

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 • 2.8k views

ADD COMMENT • link 10.8 years ago by Nicolas Rosewick 10k

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Maybe contamination with genomic DNA?

ADD REPLY • link 10.8 years ago by Michael 54k

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That was my first thought too..

ADD REPLY • link 10.8 years ago by User 59 13k

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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) ) ?

ADD REPLY • link 10.8 years ago by Nicolas Rosewick 10k

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