The setVectorParam command allows you to adjust the parameters used for vector trimming. In order to be applied, this command must appear in the script before the loadVector or TrimVector command, and the vectScan parameter for the assemble command must be set to ‘true.’
| Parameter | Description | Allowed values (defaults in bold) |
|---|---|---|
| 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 vector has been reached, and the alignment will stop. | [number from 10-1000000] Default = 100 |
| EndCutOff | The distance to the endpoint where trimming will go all the way to the end of the sequence. Wizard equivalent: Advanced Trim/Scan Options > Trim to end. | [number from 0-1000000] Default = 25 |
| EndMerMatch | The minimum number of mer matches required to start an alignment in the specified end region. | [number from 1-25] Default = 1 |
| EndRegion | The number of bases at the end of a sequence where a lower stringency for matching and trimming is used. | [number from 0-1000000] Default = 15 |
| MaxMerGap | The maximum distance between two mers required to be considered a matching pair. | [number from 0-50] Default = 5 |
| MergeTrimGap | Maximum distance between two trim segments that will cause the segments to be merged. MergeTrimGap limits trimming to the ends of sequence reads, while EndCutOff doesn’t. Controls how sensitive trimming should be in areas where some portions of the sequence match a vector and other portions don’t. The higher the number the more likely the vector trimmer will find all the vector sequence in a region of poor quality. The smaller the number, the more confidence there is that the bases trimmed are actually vector and not a spurious match. | [number from 0-1000000] Default = 7, which is suitable for trimming linkers from the ends of sequences. |
| MerLength | The minimum length of a mer required to be considered an exact match when searching for vector. Wizard equivalent: Advanced Trim/Scan Options > Mer length. | [number from 5-25] Default = 9 |
| MinEndTrimLength | The minimum length to be trimmed when a vector matches the end of a read. This parameter can be useful in preventing small spurious matches from being trimmed, which may be significant with short read technologies. | [number from 5-1000000] Default = 5 |
| MinMerMatch | The minimum number of matching mers required to start an alignment. Wizard equivalent: Advanced Trim/Scan Options > Minimum matches. | [number from 1-25] Default = 3 |
| MinTrimLength | The minimum length required for a mer to be considered as a match for vector trimming. Wizard equivalent: Advanced Trim/Scan Options > Trim length. | [number from 5-1000000] Default = 30 |
Example:
setVectorParam merLength:9
setVectorParam minMerMatch:3
setVectorParam MerGap:5
setVectorParam minTrimLength:30
setVectorParam minEndTrimLength:5
setVectorParam alignCutoff:100
setVectorParam endRegion:15
setVectorParam endCutoff:25
setVectorParam endMerMatch:1
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