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|11-18-2015, 08:30 PM||#1|
Join Date: May 2013
Nucleotide bias in RNASeq data (initial 12-13 bp)
It's a good question, and no one seems to have been able to come up with an entirely satisfactory answer.
Here is the answer from the Illumina FAQ, stating that twelve is the length of "the length of two hexameters", which is not very helpful, since I can't see how there could there be 2 hexameters binding.
This document is no longer available on Illumina's website.
Luckily, the FAQ was archived on an older seqanswers thread.
So, none of the explanations are entirely satisfactory.
What is certain is that the overall results remain valid, despite this bias.
Otherwise, one would have to question the entire body of literature on RNA-Seq.
Trimming the bases is also clearly the wrong approach.
I suppose there might be material for another paper for anyone can come up with a sound demonstration for the reason that the bias extends all the way to the first 12 (or 13) bases.
Last edited by GenoMax; 11-19-2015 at 05:50 AM.