I am confused as to why after increasing the 5' clipping penalty, I do not see an alignment with no 5' clipping promoted to be the primary, and in fact, it disappears.
So the 5' clipping is turned up to 1000, so I would expect that we get the 103S48M alignment since it has no 5' soft-clipping (sequencing order), but instead we get a strange 27S85M33I3M3D3M alignment.
The latter says it has score 78, which makes no sense:
I am confused as to why after increasing the
5'
clipping penalty, I do not see an alignment with no5'
clipping promoted to be the primary, and in fact, it disappears.So the
5'
clipping is turned up to 1000, so I would expect that we get the103S48M
alignment since it has no5'
soft-clipping (sequencing order), but instead we get a strange27S85M33I3M3D3M
alignment.The latter says it has score
78
, which makes no sense:unless you look back on the original alignment
27S78M46S
where the soft-clips are not penalized (78M
score).