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Old 06-14-2011, 04:02 PM   #1
Location: boston

Join Date: Jun 2011
Posts: 27
Default Run hundreds of BWA commands without waiting

Hi guys
I'm analyzing some high-coverage trio data. So Need to run BWA for hundreds of fastq.gz files. Obviously I should write some script to finish such task without waiting and typing in hundreds of commands one by one. But as a beginner without coding experience, I don't know how to do.

For example, I just put
bwa aln -t 24 index file1>1.sam
bwa aln -t 24 index file2>2.sam
bwa aln -t 24 index file3>3.sam

into the script, and run it..........and it doesn't work at all.
I know I must miss sth., say, the pathway for fastq files.

anyone can give any pattern about such script of executing multiple jobs? thx
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