3' Adapter stripping is used where the length of the DNA fragments being sequenced are likely to be shorter than the read length. This will be the case when selecting small, or micro, RNA for sequencing and can also happen to a lesser degree on almost any run of the Illumina GA as some small fragments will get through the Gel selection process. This stripping occurs during the alignment.
Adapter stripping does a localized alignment on the end of the reads and does allow for mismatches.
A list of standard Illumina adapters can be found at: http://seqanswers.com/forums/showthread.php?t=198
Note: The user should understand the order of operations that takes place when doing the 3' end adapter stripping during an alignment:
1. Quality trimming/other trimming options
2. Strip adapters
If a read contains any sequence representing the barcode (Multiplex Identifier (MID) ) at the end of the read, this sequence may interfere with the adapter stripping module. The 3' adapter stripping does a localized alignment at the right end of the read, but it is unable to find internal adapters.
You may remove the MID sequence using either the MID Extraction + Adapter Stripping module, or choose to trim the # of bases of the MID sequence from the end of the read using Advanced Trimming options (i.e. "Trim last nucleotides").
For situations where the adapter is at the end of the read (i.e Sequence - Barcode - Adapter, you can set TrimReadsFirst=False.
As mentioned above, AdapterStripping 3'End is unable to strip internal adapter. Please use AdapterStripping Right for such cases.