Entering edit mode
3.7 years ago
VineethVenumadhavan
▴
50
What is the difference between bowtie alignment reporting options
I) -k 1 and II) -a --best --strata
Both reports best one alignment ? If not please clarify.
option I)
if -k is 1, it will report up to 1 good alignments per read.
option II)
-a option tells bowtie to report all the alignments.
--best options tells bowtie to output all the alignments but in an increasing order of mismatches.
--strata will only report the best alignment for a read.
(source : As per bowtie1 -m --best --strata options )
