mRNA seq analysis
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
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