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RNAseq, poly(A) selection

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
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updated by Cacau Cacau • written by xd_d xd_d

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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written by WouterDeCoster WouterDeCoster

1 answer

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

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written by Cacau Cacau

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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written by xd_d xd_d

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