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mkatari-bioinformatics-august-2013-blastnotes [2014/07/02 14:12] mkatarimkatari-bioinformatics-august-2013-blastnotes [2015/06/04 12:38] (current) mkatari
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 [[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop Home]] [[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop Home]]
 +
 +This page contains a short introduction on how to create a Blast database and also how to run Blast using a query. Please replace your sequences with the names provided for the scripts to work for you.
 +
 +**Please remember** --- if you are planning to run Blast on command line, please do it in **interactive** mode. The recommended approach is to use sbatch scripts (described in more detail further down the page). 
  
 ====== Getting specific fasta sequences from reference file ====== ====== Getting specific fasta sequences from reference file ======
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 <code> <code>
 module load blast module load blast
-which blastx # note this will only work if you already have the blast module loaded. +which blastn # note this will only work if you already have the blast module loaded. 
-/export/apps/blast/2.2.28+/bin/blastx+/export/apps/blast/2.2.28+/bin/blastn
 </code> </code>
  
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 #SBATCH -n 8 #SBATCH -n 8
  
-/export/apps/blast/2.2.28+/bin/blastx -db /export/data/bio/ncbi/blast/db/nr -query /home/mkatari/ndl06-132-velvet31/contigs.fa -out /home/mkatari/ndl06-132-velvet31/contigs.fa.nr -num_threads 8 -outfmt 6 -evalue 0.00001+module load blast 
 + 
 +echo "Blast ready to run" 
 + 
 +blastn -db cassavaV5 -query scaffold12498.fa 
 +       -out scaffold12498.cassavaV5_2.bout \ 
 +       --num_threads 8 -outfmt 6 -evalue 0.00001 
 + 
 +echo "Blast complete" 
 </code> </code>
 +
  
   * Run the sbatch file. As soon as you run the file a job id will be assigned to your submission.   * Run the sbatch file. As soon as you run the file a job id will be assigned to your submission.
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 echo $OUTPUT echo $OUTPUT
  
-/export/apps/blast/2.2.28+/bin/blastx -db /export/data/bio/ncbi/blast/db/nr -query $INPUT -out $OUTPUT  -num_threads 8 -outfmt 6 -evalue 0.00001+/export/apps/blast/2.2.28+/bin/blastx 
 +    -db /export/data/bio/ncbi/blast/db/nr 
 +    -query $INPUT 
 +    -out $OUTPUT  
 +    -num_threads 8 
 +    -outfmt 6 
 +    -evalue 0.00001 
 + 
 +# the different columns in this output format are : 
 +# Fields: query id,  
 +          subject id,  
 +          % identity,  
 +          alignment length,  
 +          mismatches,  
 +          gap opens,  
 +          query start,  
 +          query end,  
 +          subject start,  
 +          subject end,  
 +          evalue,  
 +          bit score
 </code> </code>
  
mkatari-bioinformatics-august-2013-blastnotes.1404310333.txt.gz · Last modified: 2014/07/02 14:12 by mkatari