Trim by sequences in the file
The file that contains the trimming sequences is a tab-delimited text file with up to four fields:
Field | Description |
|---|---|
1st | Name |
2nd | 5’ Trim Sequence |
3rd | 3’ Trim Sequence |
4th | Option Code: • E - Exact match • L - Loose match • P - Partial match |
Loose match uses the method described in Trim by sequences with the following caveat: An input sequence with a length < 4 bp cannot be used for Loose match; however, the sequence can be used for Partial match and miRNA trimming. (See miRNA Trimming.)
In a Partial match, just a single base can be matched. Partial match allows for mismatches up to 10% of the matched length. This means the following:
• No mismatches are allowed if the adapter is < 10 bp in length or if only 10 bp of the adapter are overlapped.
• The adapter must be at the end of the read. 3’ sequences can only partially overlap at the beginning of the sequence and the end of the read while 5’ sequences can only partially overlap at the end of the sequence and the beginning of the read.
Values for the first and fourth fields are always required. Because you are trimming by sequence, you must have at least one sequence. This means that a trim sequence for either the second or third fields is required. If you have a 5’ trim sequence (second field), then the 3’ trim sequence (third field) is optional. Conversely, if you have a 3’ trim sequence (third field), then the 5’ trim sequence (second field) is optional. You still must use a placeholder if you do not have values for an optional field. For example, if you have a 5’ trim sequence (second field), but not a 3’ trim sequence (third field), then you must still enter a dash (-) in the third field, which is used as a placeholder.
 | This option is backwards-compatible with older text formats. Loose match is assumed for the Match Type. |
If both 5’ and 3’ sequences are specified, then the 5’ sequences are checked first. If multiple matches are found, then the best match for both the 5’ and 3’ ends are used for trimming.