Action to perform when a match is found
When the first match for a given adapter is found on a read sequence, the Trim tool acts based on the action specified for that adapter. There are three actions to choose from:
- Remove adapter The adapter and all the nucleotides 5' of the match are removed when a match is found. All the nucleotides 3' of the adapter match will be preserved in the read, which is retained in the trimmed reads list. If there are no nucleotides 3' of the adapter match, the read is placed in the list of discarded sequences (see Trim output).
- Discard when not found The read sequence is trimmed, as described above for the Remove adapter option, if a match is found. However, if no match is found, the read sequence is placed in the list of discarded sequences. This kind of adapter trimming is useful for small RNA sequencing where the remnants of the adapter is an indication that this is indeed a small RNA. Note that if an adapter list contains multiple adapters marked "Discard when not found", then only sequences containing all the adapters will be retained in the list of trimmed reads.
- Discard when found The read is placed in the list of discarded sequences. If no match is found, the read is retained in the list of trimmed reads. This can be used for quality checking the data for linker contamination, etc.