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Old 06-15-2010, 08:49 PM   #1
ledsall
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Location: San Diego

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

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:

Code:
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:

Code:
GAII_0001:1:1:1145:8968#0       141     *       0       0       *       *       0       0       NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN    ####################################################################################################  XM:i:0
Thank you,
Lee
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Old 06-16-2010, 12:41 AM   #2
maubp
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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.
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Old 06-16-2010, 04:27 AM   #3
colindaven
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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
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Old 02-24-2013, 12:31 AM   #4
Ettwiller
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Quote:
Originally Posted by colindaven View Post
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
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