Realistic RNA-seq using Polyester + Differences between Hexamer bias and positional bias?

Question

[shinyjj]

Hi all,

Can somebody explain the difference between hexamer bias and positional bias in RNA short reads?

I am using polyester to generate realistic RNA-seq data from the reference transcript. It would be nice for this realistic rna-seq to be illumina profiled, introducing hexamer bias, positional bias, and SNP (indels). It would be nice if someone who is good at polyester can give some example command line that introduces realistic rna-seq including the above parameters.

If there is a better tool than polyester to generate rna-seq from reference transcript, that would be great too. I am not sure how many parameters should I include in the reference transcript to generate realistic enough rna-seq data.

Thank you