RNAseq, poly(A) selection

Question

[xd_d]

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 ?

[WouterDeCoster]

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.

Answer 1

[Cacau]

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

[xd_d]

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..