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--- mkatari-bioinformatics-august-2013-blastnotes [2014/07/11 08:53] – mkatari
+++ mkatari-bioinformatics-august-2013-blastnotes [2015/06/04 12:38] (current) – mkatari
@@ Line 1: / Line 1: @@
 [[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 ======
@@ Line 54: / Line 58: @@
 <code>
 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>
@@ Line 72: / Line 76: @@
 #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>
   * Run the sbatch file. As soon as you run the file a job id will be assigned to your submission.
@@ Line 127: / Line 141: @@
     -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>