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Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | The directory to store seqpos results. | |
| Genome assembly version | UCSC database version (GENOME). | hg19 |
| Output file name | Name of the output file which stores new motifs found during a de novo search (-n). | Default |
| De novo motifs | Run de novo motif search (-d). | False |
| Motif database | Known motif collections. (-m). Warning: computation time increases with selecting additional databases. It is recommended to use cistrome.xml. It is a comprehensive collection of motifs from the other databases with similar motifs deleted. | cistrome.xml |
| Region width | Width of the region to be scanned for motifs; depends on a resolution of assay (-w). | 600 |
| Pvalue cutoff | Pvalue cutoff for the motif significance (-p). | 0.001 |
Parameters in Schema File
Type: conservation_plot seqpos-id
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| output-filedir | Output directory | string |
| titleassembly | Genome assembly version | stringlabel |
| out_name | Output file name | string |
| assemblyde_versionnovo | De novo motifs | stringboolean |
| windosmotif_sdb | Motif database | numericstringheight |
| reg_width | Region width | numericwidth |
| p_val | Pvalue cutoff | numeric |
Input/Output Ports
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