[galaxy-commits] commit/galaxy-central: jgoecks: Add parameter to Tophat2 so that output BAM is ordered using reference contigs ordering rather than sorted lexicographically.

9 Jan 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a7049f42a9d9/
changeset:   a7049f42a9d9
user:        jgoecks
date:        2013-01-09 19:36:33
summary:     Add parameter to Tophat2 so that output BAM is ordered using reference contigs ordering rather than sorted lexicographically.
affected #:  1 file

diff -r 184c5e409425da36556de7edda910a7ffe6bc9d0 -r a7049f42a9d9b4bef6804dee53a2bc8bcc1a2916 tools/ngs_rna/tophat2_wrapper.py

--- a/tools/ngs_rna/tophat2_wrapper.py
+++ b/tools/ngs_rna/tophat2_wrapper.py
@@ -134,7 +134,7 @@
         index_path = options.index_path
 
     # Build tophat command.
-    cmd = 'tophat2 %s %s %s'
+    cmd = 'tophat2 --keep-fasta-order %s %s %s'
     reads = options.input1
     if options.input2:
         reads += ' ' + options.input2

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: jgoecks: Add parameter to Tophat2 so that output BAM is ordered using reference contigs ordering rather than sorted lexicographically.

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