Basic steps in prokaryotic RNAseq data analysis

[Muhidini]

Hi all,
I have tried to browse the SEQanswers forum for my specific question but could not find anything (which does not mean it does not exist...). I am currently working on an RNASeq experiment involving prokaryotic organisms with partly finished/annotated genomes.

Davis McC (http://seqanswers.com/forums/archive...hp/t-5248.html) has made a very good attempt summarizing the basic steps in RNAseq analysis, but as far as I understood he was describing the analysis for eukaryotes.

Now my question is whether I can employ the same tools, i.e.:

1) Get short reads

2) Map reads against a reference with a short-read aligner like "bwa".

3) Summarize reads using "Rsamtools" in R. This is where I got stuck, I am not sure how to perform this basic operation- any suggestions ?

4) Calculate differential gene expression using an R-based package such as "edgeR" or "DSeq" (I have not tried this either, hints ?)

5) Perform gene-ontology category testing on differentially expressed genes using a package such as "goseq"

I hope I got these very basic steps right and would be greatful for any hints, tips & tricks, experiences using the abovementioned programs on prokaryotes.

Thanks for your help and time !
Cheers
Lars