Setting | Description |
|---|---|
Save Matched Reads | Select this option to create the <sample file name>_matched. .fasta file, which contains all the reads that aligned to the reference. |
Highlight Anchor Sequence | Applicable only when aligning condensed reads. All the anchor sequences that were used for condensation are displayed in Bold type in the Sequence Alignment window. |
Ambiguous Gain/Loss | If this option is selected, NextGENe calculates the Ambiguous Gain penalty and the Ambiguous Loss penalty for each variant call. (See Ambiguous Gain penalty/Ambiguous Loss penalty.) Note: If this option is selected, then processing time is increased. |
Detect structural variations | Select this option if you want to detect locations of possible structural rearrangements, and then click SV Settings to open the Structural Variation Settings dialog box and specify the detection settings. See Detecting structural variations in NextGENe. Note: For a detailed discussion about using NextGENe to detect structural variations, including the required preloaded reference and how to increase the length of the reads and improve alignment, see the NextGENe application note, Structural Variation Detection using NextGENe software, available from the SoftGenetics website (https://softgenetics.com/appnotes.php). |