Setting | Description |
|---|---|
miRNA Trimming | Select this option to trim miRNA reads. This function uses a trim by sequence algorithm that was specifically designed for miRNA data. It trims the input sequences only at the 3' ends of reads. It also allows for trimming where only a portion of the input sequence is found. • N/A if you have specified both 5’ and 3’ sequences in the text file loaded for Trim by sequences in the file. • Option code of Exact, Loose, or Partial match can be specified. The default is Loose. • Exact—Must match the full primer exactly anywhere in the read. • Loose—Can match as low as 80%. • Partial—Can appear as a partial sequence at the 3’ end (only if not found earlier in the read). |
Check for Primer Dimers/Trimers | Selected by default. Where the same sequence is repeated two or three times in a row, all the sequences are trimmed. Clear this option to always trim only the first sequence that is found. • If this option is selected, and you specified the following option code, then: • Exact—Can occur up to 3x length inside read. Must match exactly. Select farthest “inside” match. • Loose—Can occur up to 3x length into the read. Minimum 80% match. Select farthest “inside” match. • Partial—N/A. Processed the same as not selecting this option. • If this option is not selected, and you specified the following option code, then: • Exact—Must occur at the end of the read (5' or 3' end as specified). Must match exactly. • Loose—Can occur up to 1.5x length into the read. Minimum 80% match. Select the farthest “outside” match. • Partial—Must occur at the end of the read. Minimum 80% match. If the full sequence is not found, checks shorter portions of the sequence (end of 5' sequence or beginning of 3' sequence). Selects the match with the largest number of matching positions. As few as one bp can be found. |