The setRepeatParam command allows you to adjust the parameters used for scanning for repetitive sequences. In order to be applied, this command must appear in the script before the loadRepeat command, and the repeatScan parameter for the assemble command must be set to ‘true.’
| Parameter | Description | Allowed values |
|---|---|---|
| AlignCutoff | The minimum acceptable alignment score. When the alignment score drops below the specified value, this indicates that the end of the alignment between the read and the repeat has been reached, and the alignment will stop. | [number from 10-1000000] Default = 100 |
| MaxMerGap | The maximum distance between two mers required to be considered a matching pair. | [number from 0-50] Default = 10 |
| MerLength | The minimum length of a mer required to be considered an exact match when scanning for repeats. Wizard equivalent: Advanced Trim/Scan Options > Mer length. | [number from 5-50] Default = 17 |
| MinEndFlagLen | The minimum length required for a mer to be flagged as a repeat if the segment is bound by the end of the read. | [number from 5-1000000] Default = 25 |
| MinFlagLength | The minimum length required for a mer to be flagged as a repeat. Wizard equivalent: Advanced Trim/Scan Options > Flag length. | [number from 5-1000000] Default = 50 |
| MinMerMatch | The minimum number of matching mers required to start an alignment. Wizard equivalent: Advanced Trim/Scan Options > Minimum matches. | [number from 2-25] Default = 2 |
Example:
setRepeatParam merLength:17
setRepeatParam minMerMatch:2
setRepeatParam maxMerGap:10
setRepeatParam minFlagLength:50
setRepeatParam alignCutoff:100
setRepeatParam minEndFlagLength:25
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