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 Finds motifs enriched in a set of regions.

Parameters in GUI

ParameterDescriptionDefault value
Output directoryThe directory to store seqpos results. 
Genome assembly versionUCSC database version (GENOME).hg19
Output file nameName of the output file which stores new motifs found during a de novo search (-n).Default
De novo motifsRun de novo motif search (-d).False
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.xml
Region widthWidth of the region to be scanned for motifs; depends on a resolution of assay (-w).600
Pvalue cutoffPvalue cutoff for the motif significance (-p).0.001

Parameters in Workflow File

Type: seqpos-id

ParameterParameter in the GUIType
output-dirOutput directory

string

assemblyGenome assembly versionstring
out_nameOutput file namestring
de_novoDe novo motifsboolean
motif_dbMotif databasestring
reg_widthRegion widthnumeric
p_valPvalue cutoffnumeric

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
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