Uniquely mapped reads with bowtie

[mapper]

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]

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]

thnx ........