The splitLinkerReads command splits specified reads based on their match to given linker sequences. Reads that align to the linker and include the linker site (as specified by the linkerSite parameter or by the cloneSite option in an .fof file) will be split into two reads. The two newly split reads will be designated by _A and _B appended to the name.
| Parameter | Description | Allowed values |
|---|---|---|
| linkerFile | The directory and file name of the linker file. | [directory/filename enclosed in quotes] |
| linkerSite | The position indicating where reads should be split. | [number] |
| seqFile | The directory and file name of the sequence reads. | [directory/filename enclosed in quotes] |
Example:
splitLinkerReads
seqFile: “/Library/123_project/reads.fas”
linkerFile: “/Library/123_project/linker.fas”
linkerSite:30
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