metatranscriptome mapping

[Francy87]

Hello!
I'm sorry for the silly question, but it's the my first time managing metatranscriptomic data and I'm still confused. I have Illumina shotgun metatranscriptome from my samples. I used bowtie to map each sample to some reference genomes from NCBI and so I obtained one .sam file for each sample. My question is... how should I proceed now? I mean, what are the next steps? Moreover, how can I evaluate the quality of the mapping?
Thanks!!

[AdrianP]

Try a denovo transcriptome assembly with oases or a similar tool? The program will build contigs that represent transcripts. Use blast2go to annotate those transcripts. Figure out how many organisms you got in each sample.

Try some tblastx between samples to see what genes are expressed in some samples but not others.

[Francy87]

Hi Adrian!
What I'd like to obtain is a sort of table with the gene annotations and the relative abundance in each sample. Starting from my sam files, how could I get this?
I'm sorry, but I'm quite confused!