1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f0e26a4f7dd9/ changeset: f0e26a4f7dd9 user: jgoecks date: 2012-08-22 22:49:12 summary: Output sorted BAM from Bowtie2. affected #: 1 file
diff -r 695159af542b44ac5038d1b3cc401b3f4b98d2e3 -r f0e26a4f7dd91d9a632913ae450e285e37a9a302 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -64,8 +64,8 @@ else: index_path = options.index_path
- # Build bowtie command. - cmd = 'bowtie2 %s -x %s %s | samtools view -Sb - > %s' + # Build bowtie command; use view and sort to create sorted bam. + cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - sorted > %s'
# Set up reads. if options.single_paired == 'paired':
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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