Question: Understanding Bowtie output
gravatar for am3
16 months ago by
am370 wrote:


I'm using bowtie2 to align some whole-exome sequencing reads and have a basic question about the output I get.

The summary text includes the line X% aligned concordantly >1 times. In my files, X is generally pretty high (40% or so).

However, I did not specify -k or -a when I ran the program, which as far as I understand means the program should be reporting 1 alignment per read, NOT reporting "all valid alignments." How am I then getting so many reads that align more than once?

Am I misunderstanding what is meant by "aligned concordantly >1 times" or by what is meant by "report 1 valid alignment"?

Thank you!

bowtie alignment • 373 views
ADD COMMENTlink modified 16 months ago by manuel.belmadani1.2k • written 16 months ago by am370
gravatar for manuel.belmadani
16 months ago by
manuel.belmadani1.2k wrote:

From the bowtie2 manual:

Default mode: search for multiple alignments, report the best one


When it finds a valid alignment, it generally will continue to look for alignments that are nearly as good or better. It will eventually stop looking, either because it exceeded a limit placed on search effort (see -D and -R) or because it already knows all it needs to know to report an alignment.

So the summary text is probably just be reporting the runtime statistics as described above, not what's (reported) in your output files. You could check your SAM file to see if that's true.

ADD COMMENTlink modified 16 months ago • written 16 months ago by manuel.belmadani1.2k
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