Dear Biostars,
I'm slightly confused by the way Bowtie reports reads that align to multiple locations. If I understand correctly from the manual, by default only 1 alignment is returned (-k 1). But this may not necessarily be the best alignment, because then --best must be specified as well. So is this a random or just a 'good' alignment? And what is the difference with -M 1? According to the manual this gives 1 random alignment from the best alignments, but is this not the same as -k 1?
Kinds regards,
Sander
1 answer
-k is not related to 'best' alignment. -k is related to multimapped reads. A read may map at various places with v.high quality/best mapping, but only one position is reported by default.
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GouthamAtla
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