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--- mkatari-bioinformatics-august-2013-blastnotes [2014/07/02 14:12] – mkatari
+++ mkatari-bioinformatics-august-2013-blastnotes [2014/07/11 09:04] – mkatari
@@ Line 120: / Line 120: @@
 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>