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
-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"?