I'm using bowtie2 to map a FASTQ file of reads from an Illumina MiSeq to some reference sequences, and I'm trying to understand the difference between discordant and mixed pairs.
In the bowtie2 manual, it describes discordant pairs as having the two reads in unexpected relative positions. For example, the reverse read earlier than the forward read, or the two reads too far apart.
The manual just says that mixed mode will try to map the individual reads separately if they fail to map as a pair. However, when I compare a pair that will only map in mixed mode with a pair that maps discordantly, I can't see any difference. They both just have a base or two extra on the reverse read that extends past the start of the forward read.
What stops a pair of reads from mapping together?
I'm using the --local option, if that's important, and I do see soft clipping.
