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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?
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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.Last edited by blancha; 11-13-2015, 07:50 PM. -
Thanks, that helps a lot.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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