Finds motifs enriched in a set of regions.
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 Workflow File
Type: seqpos-id
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| output-dir | Output directory | string |
| assembly | Genome assembly version | string |
| out_name | Output file name | string |
| de_novo | De novo motifs | boolean |
| motif_db | Motif database | string |
| reg_width | Region width | numeric |
| p_val | Pvalue cutoff | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: SeqPos data
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Input regions | cp_treat-ann | ann-table-list |