Entering edit mode
3.2 years ago
Wöps ▴ 10
my RNA-seq reads seem to be slighly biased to show more 'T' than 'A' (see image). This is unexpected for me. Does anyone have a suggestion why that might be (and how to proceed)?
The data are paired-end, sequenced with Illumina HiSeq 2500. (The read direction is reverse.)
thanks for your help!
Your image doesn't work but also something to think about is that the most RNA-seq technologies sequence the cDNA (reverse transcribed copy) of your mRNA molecules. Thus assuming the method is strand-specific the poly-A tails will often look like stretches of T's; potentially explaining your results.
Fixed the link to the image. Please use the image button and paste in the full link incl. the suffix (e.g.
.png) into the field that pops up:
Thank you! Will do next time.
Have you trimmed off poly-A sections?
I hadn't trimmed poly-A sections so far. I now quickly tried running afterQC (https://github.com/OpenGene/AfterQC) to remove any reads with polyX above length 20. It does not seem to change the situation though:
As genomax says, what you see is normal. Just proceed with your analysis.