The fixedTrim command trims reads prior to assembly using fixed values. Based on the parameter settings for this command, SeqMan NGen will trim reads either by a specified number of bases from each end, or to a specified range.
| Parameter | Description | Allowed values |
|---|---|---|
| end3 | If trimRelative (see below) is set to ‘true,’ then this value indicates the number of bases for SeqMan NGen to trim from the 3’ end of each read. If trimRelative is set to ‘false,’ then this value indicates the specific 3’ coordinate to which reads should be trimmed. Wizard equivalent: Advanced Trim/Scan Options > 3’ trim. | [number from 0-1000000] Default = 0 |
| end5 | If trimRelative (see below) is set to ‘true,’ then this value indicates the number of bases for SeqMan NGen to trim from the 5’ end of each read. If trimRelative is set to ‘false,’ then this value indicates the specific 5’ coordinate to which reads should be trimmed. Wizard equivalent: Advanced Trim/Scan Options > 5’ trim. | [number from 0-1000000] Default = 0 |
| trimRelative | Specifies whether the value for the end3 and end5 parameters should indicate the number of bases for SeqMan NGen to trim from the 3’ or 5’ end of each read. When ‘false,’ the value specified for the end3 or end5 parameter indicates the specific coordinate to which reads should be trimmed. | [ true / false ] |
Example:
fixedTrim
end5:10
end3:20
trimRelative:true
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