Finds motifs enriched in a set of regions.

Element type: seqpos-id

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output directoryThe directory to store seqpos results.
output-dir

string

Genome assembly versionUCSC database version (GENOME).hg19assemblystring
Output file nameName of the output file which stores new motifs found during a de novo search (-n).Defaultout_namestring
De novo motifsRun de novo motif search (-d).Falsede_novoboolean
Motif databaseKnown 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.xmlmotif_dbstring
Region widthWidth of the region to be scanned for motifs; depends on a resolution of assay (-w).600reg_widthnumeric
Pvalue cutoffPvalue cutoff for the motif significance (-p).0.001p_valnumeric

Input/Output Ports

The element has 1 input port:

Name in GUI: SeqPos data

Name in Workflow File: in-data

Slots:

Slot In GUISlot in Workflow FileType
Input regionscp_treat-annann-table-list