Bowtie output and reference genome question

[jpmatteson]

Hello, a quick question for anybody familiar with bowtie. In my reference genome files, which have names like SVID_XXX, the first line of text, before the actual sequence data is a line like >Chromosome, or >ContigXXXX, .... In the bowtie output data, Chromosome or ContigXXXX shows up as the file name it mapped to instead of SVID_XXX, the actual file name. My question is this, is bowtie taking the > symbol in the first line of text as a command to redirect to this file name or whatever comes after it in that line? I know that > redirects output to a file, but why does this happen in bowtie since the file already has a file name, and > only shows up in the first line of a text file? I hope this makes sense, any thoughts?

[blancha]

Your reference genome files are FASTA files.

The FASTA file format is simple.
There is one line, starting with the symbol ">" which describes the sequence.
The first word after ">" is the name of the sequence.
Following the sequence description is the sequence itself.

Bowtie and all programs dealing with raw genomic data are written to be able to parse FASTA files.

The FASTA format has nothing to do with the Unix redirection operator, and dates back to 1985.

[jpmatteson]

Thanks, that helps a lot.