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If I align with Bowtie and use the option -m 3 and default settings for everything else, and a read has 2 valid and equally well-aligning alignments, what is reported? Both alignments? The default setting -k 1 implies that only 1 alignment will ever be reported per read so will one be chosen at random? I know that if a sequence has >3 then nothing will be reported for that sequence.
I'm also wondering why the default setting for -m would be "no limit". Wouldn't you usually want to use a low number?
[Edit] Ok I think it will just report whichever alignment of the two it comes across first. If --best is specified and one is better it will report the better of the two. Assuming this is correct, what happens for paired-end alignments where --best is not applicable? If the two alignments are equal, the first will be reported, if one is better, then what?
I'm also wondering why the default setting for -m would be "no limit". Wouldn't you usually want to use a low number?
[Edit] Ok I think it will just report whichever alignment of the two it comes across first. If --best is specified and one is better it will report the better of the two. Assuming this is correct, what happens for paired-end alignments where --best is not applicable? If the two alignments are equal, the first will be reported, if one is better, then what?