The join command currently just takes the union of positions and reads kept. While this is useful for joining non-overlapping amplicons, it will not treat primer binding sites correctly if the amplicons overlap. This problem occurs because there is no way currently to use the positions for the original datasets (which would mask out the primer binding sites) only the union of the positions in all datasets (which would include the primer binding sites if the amplicons overlap).
matthewfallan
commented
5 months ago
The
joincommand currently just takes the union of positions and reads kept. While this is useful for joining non-overlapping amplicons, it will not treat primer binding sites correctly if the amplicons overlap. This problem occurs because there is no way currently to use the positions for the original datasets (which would mask out the primer binding sites) only the union of the positions in all datasets (which would include the primer binding sites if the amplicons overlap).