comparison of Illumina libraries

[PFS]

I would like to compare different library prep kits for RNA-Seq. I assume each has specific biases, but how do I proceed? In other words, from a bioinformatics point of view, what can I do besides aligning the reads to the reference genome?

Thanks!

[adarob]

Cufflinks now corrects for library-specific biases. The details, as well as examples of the different biases for different protocols (see the supplement) can be found in http://genomebiology.com/2011/12/3/R22/abstract

I would also recommend looking at this paper: http://www.nature.com/nmeth/journal/...meth.1491.html. It compares several strand-specific RNA-seq protocols. The bias for these same datasets are analyzed in the paper above.

Cufflinks 1.0, which will be released in the not too distant future, will allow you to output the sequence and positional bias for a given dataset, which should help in your analysis as well.