Action to perform when a match is found
For each read sequence in the input to trim, the Workbench performs a Smith-Waterman alignment [Smith and Waterman, 1981] with the adapter sequence to see if there is a match (details described below). When a match is found, the user can specify three kinds of actions:
- Remove adapter. This will remove the adapter and all the nucleotides 5' of the match. All the nucleotides 3' of the adapter match will be preserved in the read that will be retained in the trimmed reads list. If there are no nucleotides 3' of the adapter match, the read is added to the List of discarded sequences (see Trim output).
- Discard when not found. If a match is found, the adapter sequence is removed (including all nucleotides 5' of the match as described above) and the rest of the sequence is retained in the list of trimmed reads. If no match is found, the whole sequence is discarded and put 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.
- Discard when found. If a match is found, the read is discarded. 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 contaminations etc.