Entering edit mode
4.4 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 )