Bowtie --sam option - includes non-aligned reads?

[ledsall]

I am running Bowtie (0.12.5) with the --sam option. The output file contains non-aligned reads. I thought the SAM file was only supposed to contain aligned reads? Am I doing something wrong?

Here is the command I'm running:

bowtie -p 4 -t -a --solexa1.3-quals --minins 0 --maxins 500 -m 5 --sam ./bowtie_indexes/hg18 -1 foo1 -2 foo2 > output.txt

Here is one of the lines I'm referring to:

GAII_0001:1:1:1145:8968#0       141     *       0       0       *       *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN    ####################################################################################################  XM:i:0

Thank you,
Lee

[maubp]

SAM and BAM files can hold both aligned reads and unaligned reads, and it can be useful to have the alignment output file contain both.

[colindaven]

You're right Lee. I find it annoying as well.

It's not too tricky to write a perl script to exclude the unaligned reads though. Remember to keep the header !

Colin

[Ettwiller]

You're right Lee. I find it annoying as well.

It's not too tricky to write a perl script to exclude the unaligned reads though. Remember to keep the header !

Colin

Or you can run the following command :
samtools view -S -F0x4 test.sam > test_mapped_reads.sam