[galaxy-user] Pipeline design for bacterial RNA-Seq

Hi community,

I have just discovered a wonderful Galaxy server for RNA-Seq analysis: Oqtans http://galaxy.raetschlab.org/. I am impressed by the huge quantity of useful tools that they have integrated there.

I'm dealing with bacterial transcriptome analysis. We have the genome sequence of this bacteria.

RNA samples are now been sequenced and I am designing a pipeline for data analysis. I would like you to suggest me the tools that I can/should use in order to analyse my data. My sequences come from Ion Torrent platform. For each sample I have a fastQ file of about 3 million sequences. They are less than 200 bp and have a mean of 150 bp. I you need more information please ask me.

Thank you very much for your help. Regards, Bernardo