Uniquely mapped reads with bowtie

mapper · 11-22-2010, 09:49 PM

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...

frozenlyse · 11-22-2010, 10:55 PM

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;

mapper · 11-22-2010, 11:44 PM

thnx ........

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11-22-2010, 09:49 PM	#1
mapper Member Location: India Join Date: Nov 2010 Posts: 17	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...

11-22-2010, 10:55 PM	#2
frozenlyse Senior Member Location: Australia Join Date: Sep 2008 Posts: 136	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;

11-22-2010, 11:44 PM	#3
mapper Member Location: India Join Date: Nov 2010 Posts: 17	thnx ........