At the bottom of the dialog, you can specify how Non-specific matches
should be treated. The concept of Non-specific matches refers to a situation where a read aligns at more than one position with an equally good score
. In this case you have two options:
- Random. This will place the read in one of the positions randomly.
- Ignore. This will not include the read in the final mapping.
Note that a read is only considered non-specific when the read matches equally well at several alignment positions. If there are e.g. two possible alignment positions and one of them is a perfect match and the other involves a mismatch, the read is placed at the position with the perfect match and it is not marked as a non-specific match.
For paired data, reads are only considered non-specific matches if the entire pair could be mapped elsewhere with equal scores for both reads, or if the pair is broken in which case a read can be categorized as non-specific in the same way as single reads (see Mapping paired reads).
When looking at the mapping, the default color for non-specific matches is yellow.