Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013-blastnotes [2014/10/23 19:57] – mkatari
+++ mkatari-bioinformatics-august-2013-blastnotes [2015/06/04 12:38] (current) – mkatari
@@ Line 3: / Line 3: @@
 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.
-<strong>Please remember</strong> --- if you are planning to run Blast on command line, please do it in <strong>interactive</strong> mode. The recommended approach is to use sbatch scripts (described in more detail further down the page).
+**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 58: / 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 76: / 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.