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Old 04-27-2012, 08:51 AM   #1
Location: ND, USA

Join Date: Oct 2011
Posts: 27
Default Standalone BLAST output format question

I'm using stand-alone BLAST to align transcripts I've assembled of a non-model species to the drosophila transcriptome. I want my output to be a CSV file that includes the actual NAME of the gene. Those names are listed in the standard blast output, but I can't figure out what switch to use to get it into the CSV.

The best I can do right now is get a sequence id- something like FBtr072340098, which I can search default blast output for and find the names manually...

My command line looks something like:

blastn -query sep-final.fasta -db dmel.fasta -out sepxdmel.csv -outfmt '10 qseqid sseqid qseq evalue length'

What I really want is a CSV that has something like:


Which will make it easy for my labmates who don't do this kind of computer work to have an easy file they can search for a gene name to find a sequence to make primers and probes.

Any advice?
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