Finds motifs enriched in a set of regions.
Element type: seqpos-id
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output directory | The directory to store seqpos results. | output-dir | string | |
| Genome assembly version | UCSC database version (GENOME). | hg19 | assembly | string |
| Output file name | Name of the output file which stores new motifs found during a de novo search (-n). | Default | out_name | string |
| De novo motifs | Run de novo motif search (-d). | False | de_novo | boolean |
| 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 | motif_db | string |
| Region width | Width of the region to be scanned for motifs; depends on a resolution of assay (-w). | 600 | reg_width | numeric |
| Pvalue cutoff | Pvalue cutoff for the motif significance (-p). | 0.001 | p_val | 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 |