Difference between revisions of "Parsing Blast Results from Your Favorite Database"
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#Run your search using the command<pre>/usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send"</pre> | #Run your search using the command<pre>/usr/local/ncbi/blast/bin/blastn -query scf1453.fasta -db bb_latest_assembly.fasta -outfmt "7 qacc sacc evalue qstart qend sstart send"</pre> | ||
| + | What does this command do? | ||
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#Download blastParse.py | #Download blastParse.py | ||
#Place blastParse.py into the same folder as your blast results file | #Place blastParse.py into the same folder as your blast results file | ||
#Open terminal and navigate into the folder containing blastParse.py using following Unix commands<pre>cd OR ls</pre> | #Open terminal and navigate into the folder containing blastParse.py using following Unix commands<pre>cd OR ls</pre> | ||
#Run blastParse.py using the command <pre>python blastParse.py</pre> | #Run blastParse.py using the command <pre>python blastParse.py</pre> | ||
Revision as of 16:13, 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"
What does this command do?
- 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 following Unix commands
cd OR ls
- Run blastParse.py using the command
python blastParse.py
