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 Finds motifs enriched in a set of regions.

Element type: seqpos-id


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


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


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