Hi all
I have a doubt about -k option in bowtie 1. According to the bowtie manual, this option is used to report up to n alignments, where n is the number given to -k.
I pose this scenario,
Bowtie configuration : -k 1 -- best
If I had, for example, a read with 5 valid alignments, and two of these aligments have the same score (best score).
Bowtie has to report best of these 5 alignments, but two of them are the best.
Does bowtie report these two alignments or choose one at random?
Thanks in advance!
I have a doubt about -k option in bowtie 1. According to the bowtie manual, this option is used to report up to n alignments, where n is the number given to -k.
I pose this scenario,
Bowtie configuration : -k 1 -- best
If I had, for example, a read with 5 valid alignments, and two of these aligments have the same score (best score).
Bowtie has to report best of these 5 alignments, but two of them are the best.
Does bowtie report these two alignments or choose one at random?
Thanks in advance!
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