The splitPairs command is used to split 454 or ion torrent mate pair files into forward and reverse (and singleton) files.
| Parameter | Description | Allowed value |
|---|---|---|
| destination | The location and filename for the output. | [directory/filename enclosed in quotes] |
| DiscardLinkerless | Specifies that reads without a linker sequence should be discarded from the assembly. | [ true / false ] |
| file, reads | The location and filename for the input. | [directory/filename enclosed in quotes] |
| seqTech | Specifies the offset to be used when converting compressed quality scores into numerical values. These are the offsets used for the technology specified: Data Type / Value / Offset IonTorrent / IonTorrent / 33 Applied Biosystems SOLiD / SOLiD / 33 Illumina / Illumina / 64 Roche 454 / 454 / 33 Other types / normalScore / 33 Wizard equivalent: Input Sequence Files > Read technology. Note 1: For 454,quality scores for homopolymeric runs of ≥ 2 are oriented from 5’ to 3’ on the top strand. Note 2: If possible, the data type of unknown data is determined automatically based on the first data file. |
[IonTorrent|SOLiD|Illumina|454|normalScore|Other] |
Example:
SplitPairs
destination:”c:data\splitReads\”
reads: {
{ file:”C:data\reads\file1.fas” format: IonTorrent }
{ file: “C:data\reads\file2.fas” format:454 discardLinkerless: true}
}
Need more help with this?
Contact DNASTAR