Difference between revisions of "Parsing Local Blast Results from your favorite database"
From GcatWiki
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#Run your search using the command | #Run your search using the command | ||
/usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" | /usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send" | ||
| + | #Download blastParse.py | ||
| + | #Place blastParse.py into the same folder as your blast results file | ||
| + | #Open terminal and navigate into the folder containing blastParse.py using cd and ls commands | ||
| + | #Run blastParse.py using the command python blastParse.py | ||
Revision as of 15:29, 23 February 2011
This tutorial assumes the user has blast version __________ installed and has already made their local blast database (on their computer). It is also written for mac users, however all scripts and tools mentioned here are windows compatible with windows.
- Run your search using the command
/usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send"
- Download blastParse.py
- Place blastParse.py into the same folder as your blast results file
- Open terminal and navigate into the folder containing blastParse.py using cd and ls commands
- Run blastParse.py using the command python blastParse.py
