Bowtie - only keeping mapped reads.

[susanklein]

Hi,

I am trying to map a moderate set of reads, 30M, to a small set of genes I am interested in (only 5kb or so, to find snps). So most of the data is unmapped and redundant. I want bowtie2 to output only the mapped reads, it seems ridiculous to have a 15 Gb sam file for only a few hundred mapped reads. I have tried using --no-unal but it doesn't seem to make any difference. this works:

samtools view -F 0x04 -b infile.bam > outfile.bam

but it would seem to make much more sense to get bowtie2 to only output mapped reads.

Does anyone know what I might be doing wrong.. or perhaps I should give up and use bbmap..

Thanks,

S.

[GenoMax]

--no-unal should work with Bowtie2 (see thread below). Otherwise BBMap is the way to go.

http://seqanswers.com/forums/showthread.php?t=42965

[blancha]

Check that you have the latest version of Bowtie2

You can also pipe the output of Bowtie2 to samtools view in one command, but it shouldn't be necessary.

bowtie2 -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."

http://seqanswers.com/forums/showthread.php?t=22230