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Old 01-04-2012, 03:15 AM   #1
afadda
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Location: Qatar

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Default Bowtie reporting on number of reads

Hi,
is there away to have bowtie report the summary of reads processed and aligned to a file?
thanks,
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Old 01-04-2012, 03:35 AM   #2
hanshart
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Hi,
you can simply redirect the output to a file using
Quote:
> output.txt
after the bowtie call

or you can use the pipe (|) and shell commands like grep, head, tail, awk etc. to filter the output. e.g.
Quote:
...| grep "aligned reads" > output.txt

Last edited by hanshart; 01-04-2012 at 03:37 AM.
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