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mapping bacteria metatranscriptome to genomes
Hello! I'm pretty new to rna-seq data analysis and I'm not sure about how proceed with it.
I have bacteria metatranscriptome reads from environmental samples and I know more or less which species are present. So I'd like to try to map them to some genomes (those of the species I know that should be there), using bowtie. I don't know about where to find the genomes and which file formats I need. I'm wandering about downloading them from here ftp://ftp.ncbi.nih.gov/genomes/Bacteria/, but for each genome there are a lot of different files. As I could understand, I need .ffn to build the bowtie index (if I want to use only the protein coding parts of the genomes). But then, in which file do I find the corresponding gene annotations (so the names of the genes)?
thanks
Francesca
I have bacteria metatranscriptome reads from environmental samples and I know more or less which species are present. So I'd like to try to map them to some genomes (those of the species I know that should be there), using bowtie. I don't know about where to find the genomes and which file formats I need. I'm wandering about downloading them from here ftp://ftp.ncbi.nih.gov/genomes/Bacteria/, but for each genome there are a lot of different files. As I could understand, I need .ffn to build the bowtie index (if I want to use only the protein coding parts of the genomes). But then, in which file do I find the corresponding gene annotations (so the names of the genes)?
thanks
Francesca