Naming isomiRs
The names of aligned sequences in mature groups adhere to a naming convention that generates unique names for all isomiRs. This convention is inspired by the discussion available here: https://github.com/miRTop/incubator/blob/master/isomirs/isomir_naming.md
Deletions are in lowercase and there is a suffix s for 5' (figure 12.9):
Figure 12.9: Naming of deletions.
Insertions are in uppercase and there is a suffix s for 5' (figure 12.10):
Figure 12.10: Naming of insertions.
Note that indels within miRNAs are not supported.
Mutations (SNVs) are indicated with reference symbol, position and new symbol. Consecutive mutations will not be merged into MNVs. The position is relative to the reference, so preceding (5') indels will not offset it (figure 12.11):
Figure 12.11: Naming of mutations.
Deletions followed by insertions will be annotated as in figure 12.12:
Figure 12.12: Naming of deletions followed by insertions.
If a read maps to multiple miRBase sequences we will add the suffix `ambiguous' to its name. This can happen when multiple species are selected, as they will often share the same miRBase sequence, or when a read does not map perfectly to any miRBase sequence, but it is close to two or more, distinguished by just one SNV for example.