RNAseq, poly(A) selection
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7.0 years ago
xd_d ▴ 110

Hello all,

I have analyze some poly(A) RNAseq data. And I often see that a lot of reads are within intronic region.

Has anybody an idea, what these annotated Elements are. Maybe SINE or LINE Elements ?

RNA-Seq next-gen sequencing • 1.7k views
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Any chance that this is DNA contamination? Was a DNase treatment performed?
PolyA stretches in gDNA may lead to capture by polyT beads and incorporation in the library.

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7.0 years ago
Cacau ▴ 520

What species are you analyzing? May the annotation of genome be problematic?

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From the human, RNAseq from brain tumor. I use a annotation from GENCODE v25. including protein coding genes and genes of lncRNA. I use the intron coodinates to search significant peaks on the introns. And I found many..

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