random hexamer bias

[Mali Salmon]

Hello list
Do you know if HTSeq/DESeq or edgeR account for the random hexamer bias?
If not, what would be an easy way to normalize for that bias prior of running DESeq?
Thanks
Mali

[dpryan]

They don't, but normally the bias is more or less the same in all of your samples. You can, however, have a look at the cqn package, which is geared more toward GC bias, but could probably be used to deal with this issue (you can't use it with DESeq, but DESeq2 would work).

[Mali Salmon]

Thanks dpryan for your reply.
The reason I am interested with normalizing for that bias is because I have two different patterns of this bias in my samples.
I looked at the cqn package and as you said it deals with GC bias. I don't see how it would work for the hexamer bias (do you have by a change a sample R code that would do the trick?)
Thanks again
Mali