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Old 11-22-2010, 08:49 PM   #1
mapper
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Default Uniquely mapped reads with bowtie

Hi all

Is there anyway to report only mapped tags in bowtie sam output?

I tried to map reads with bowtie with -m 1 --best and --strata parameter but in mapping output(sam) reads which are not aligned are also reported...
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Old 11-22-2010, 09:55 PM   #2
frozenlyse
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I filter them out using samtools whilst converting to BAM on the fly eg

bowtie -m 1 --your-other-settings - | samtools view -F 4 -S -b - > output.bam;
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Old 11-22-2010, 10:44 PM   #3
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thnx ........
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