Obtain file from Bowtie containing only aligned reads in SAM format

[shanebrubaker]

Hi, I have been using bowtie with the -S option to align reads to a reference sequence, and get SAM file as the output.

What I want is to get ONLY the aligned reads in the output. Instead I get all of the reads, both aligned and unaligned, in a huge sam file.

I do not see an option to do this. I see an option to create an additional file of aligned reads, but it is not in sam format.

Does anyone know how to do this?

Thanks,
Shane

[mnkyboy]

You will have to post-process your SAM file after bowtie:

http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ

I want to get `unique' alignments from SAM/BAM.

We prefer to say an alignment is `reliable' rather than `unique' as `uniqueness' is not well defined in general cases. You can get reliable alignments by setting a threshold on mapping quality:
samtools view -bq 1 aln.bam > aln-reliable.bam
You may want to set a more stringent threshold to get more reliable alignments.

[swbarnes2]

You should be in SAM format as little as possible, because it's so huge. You should be piping your bowtie output into samtools, and converting them into bams on the fly.

bowtie -S whatever | samtools view -bSF4 - > mapped.bam

-b means that you want to output to be .bam -S means that the input is .sam -F4 means that reads that have the 4 flag will not be included. That'll be the mapped reads.