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--- mkatari-bioinformatics-august-2013-blastnotes [2013/08/14 11:37] – [Run Blast using sbatch] mkatari
+++ mkatari-bioinformatics-august-2013-blastnotes [2014/07/02 13:58] – mkatari
@@ Line 1: / Line 1: @@
-[[mkatari-bioinformatics-august-2013|Manny's Bioinformaics Workshop]]
+[[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop Home]]
+====== Getting specific fasta sequences from reference file ======
+In case you need to retrieve a specific sequence from a larger fasta file, use one of my perl scripts. Simply provide a pattern that it needs to match in the definition field and it will retrieve the sequence. The **-f** is the reference file, **-o** is the output file name, and **-query** is the pattern it will try to match.
+<code>
+perl /home/mkatari/PerlScripts/getFastaName.pl -f ../blast/Mesculenta_147_v4 \
+    -o scaffold12498.fa \
+    -query scaffold12498
+</code>
+====== Creating the blast database ======
+Before we can actually perform the blast, we need to prepare the database using **makeblastdb**.
+<code>
+makeblastdb -in cassavaV5 -input_type "fasta" -dbtype "nucl"
+</code>
 ====== Run Blast using sbatch ======
@@ Line 90: / Line 108: @@
 Now to refer to the value saved in the variables we simply put $ infront as shown in the blast command line.
+To execute this sbatch file you would simply provide the name of the input file as shown below.
+<code>
+sbatch /home/mkatari/blast.sbatch /home/mkatari/ndl06-132-velvet31/contigs.fa
+</code>