Understanding Bowtie output

Question

[am3]

Hello,

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!

Answer 1

[mbelmadani]

From the bowtie2 manual:

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

and

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.