BLAST: Difference between revisions

BLAST (view source)

Revision as of 20:54, 13 December 2019

45 bytes removed , 4 years ago

m

Use faSplit instead

Coulombc

cc_staff

284

edits

@@ Line 47: / Line 47: @@
 ==== Preprocessing ==== <!--T:16-->
 In order to accelerate the search, the <tt>seq.fa</tt> file must be split into smaller chunks. These should be at least <tt>1MB</tt> or greater, but '''not smaller''' as it may hurt the parallel filesystem.
-<!--T:17-->
-'''Important''': To correctly split a FASTA format file, it must be in its original format and not in multiline format. In other words, the sequence must be on a single line.
 <!--T:18-->
-Using the <tt>split</tt> utility:
+Using the <tt>faSplit</tt> utility:
-{{Command|split -d -a 1 -l 2 seq.fa seq.fa.}}
+{{Command|module load kentutils/20180716}}
-will create 10 files named <tt>seq.fa.N</tt> where <tt>N</tt> is in the range of <tt>[0..9]</tt> for 10 queries (sequences).
+{{Command|faSplit sequence seqs.fa 10 seq}}
+will create 10 files named <tt>seqN.fa</tt> where <tt>N</tt> is in the range of <tt>[0..9]</tt> for 10 queries (sequences).
 ==== Job submission ==== <!--T:19-->
@@ Line 102: / Line 100: @@
 See also [[GNU Parallel#Handling_large_files|Handling large files]] in the GNU Parallel page.
+==== Running with multiple cores on one node====
 <!--T:34-->
 {{File
@@ Line 137: / Line 136: @@
 Note: The file must not be compressed.
-==== Job submission ==== <!--T:31-->
+===== Job submission ===== <!--T:31-->
 With the above submission script, we can submit our search and it will run after the database has been created.
 {{Command|sbatch --dependency{{=}}afterok:$(sbatch makeblastdb.sh) blastn_gnu.sh}}
+==== Running with multiple cores on one node====
 === Additional tips === <!--T:32-->