I'm using bowtie in repetitive regions and need all possible alignments of these reads. My question is about the backtracking mentioned in the original bowtie paper, http://genomebiology.com/2009/10/3/R25. If I understand correctly the algorithm limits the number of backtracking steps to 125. That means that you get all valid alignments for 125 strings? Is this still the case? Is this irrelevant if you are only allowing 0-1 mismatches?
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Assuming you're using the --all option:
In -n mode (quality-aware) you can specify --tryhard to get all (?) the alignments. Not sure if it guarantees all of them, but the manual claims maximum sensitivity with that.
In -v mode (ignore quals) it'll always report all the alignments (implied by the manual).
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