mRNA seq analysis

[Francy87]

Hi!
I just started with metatranscriptome analysis, so I'm sorry to do a stupid or obvious question... I have metatranscriptome data from food fermentations, obtained through HiSeq. I already analysed the 16S data and so I know the microbiota is not very complex. Reading some other posts and some tutorials, I suppose the first thing to do is mapping them to some reference genomes, using software like bowtie... The question is: since I have reads supposed to be from many different microorganisms, is there a way to map them to more than one genome? Or should I need to map my reads to one organism at the time? If yes, then how can I assemble the files from each genome mapping?
Can someone suggest me a good pipeline to do this kind of analysis?

Thanks a lot
Francesca

[GenoMax]

I guess you just reposted this question in a new forum. Since no one has responded so far to your other post I will get the discussion started.

Are you aware of the MG-RAST? (http://metagenomics.anl.gov/) You could potentially try that for your dataset.

Another option could be to just use the genomes that you have identified by your 16S analysis and assemble reads that map to those genomes. A significant fraction of reads may end up being in multiple assemblies since there is no way to accurately classify them. If this would be a problem or not would depend on what your ultimate goal is for this analysis.

[Francy87]

Yes, I know about MG-RAST... but someone told me it can't work well with low coverage... as I have... So I'm trying to find a different way. Which software do you suggest to use for microbial metatranscriptome assebly?