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Output sorted BAM from Bowtie2.

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Jeremy Goecks
2012-08-22 16:49:12 -04:00
parent 0b2e939d4d
commit 41682ee6c9
1 changed files with 2 additions and 2 deletions
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tools/sr_mapping/bowtie2_wrapper.py
+2 -2
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@@ -64,8 +64,8 @@ def __main__():
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':