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Old 06-09-2010, 03:04 PM   #1
jtladner
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Default Alternative Hits in BWA generated .sam

I am working with Illumina sequences that are about 76 bp long. I have been looking through some .sam files generated by samse after aligning to a reference using bwa. I noticed that many of the reads that contain multiple optimal hits do not have XA tags at the end of the line, while many others do.

I have not noticed any consistent difference between reads that have the XA tag and those that don't. Can anyone offer insight into this?

Jason
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Old 06-09-2010, 03:07 PM   #2
nilshomer
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Quote:
Originally Posted by jtladner View Post
I am working with Illumina sequences that are about 76 bp long. I have been looking through some .sam files generated by samse after aligning to a reference using bwa. I noticed that many of the reads that contain multiple optimal hits do not have XA tags at the end of the line, while many others do.

I have not noticed any consistent difference between reads that have the XA tag and those that don't. Can anyone offer insight into this?

Jason
Did you check the BWA manual?
Code:
samse 	bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>

Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.

OPTIONS:
-n INT 	Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]
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