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It provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study.

Element type: ceas-report


ParameterDescriptionDefault valueParameter in Workflow FileType
Output report filePath to the report output file. Result for CEAS analysis.


Output annotations fileName of tab-delimited output text file, containing a row of annotations for every RefSeq gene. (file is not generated if no peak location data is supplied).
Gene annotations tablePath to gene annotation table (e.g. a refGene table in sqlite3 db format (--gt).hg19anns-tablestring
Span sizeSpan from TSS and TTS in the gene-centered annotation (base pairs). ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates in promoter and downstream (--span).3000spannumeric
Wiggle profiling resolutionWiggle profiling resolution. WARNING: Value smaller than the wig interval (resolution) may cause aliasing error. (--pf-res).50profiling-resolutionnumeric
Promoter/downstream intervalPromoter/downstream intervals for ChIP region annotation are three values or a single value can be given. If a single value is given, it will be segmented into three equal fractions (e.g. 3000 is equivalent to 1000,2000,3000) (--rel-dist).3000promoter-sizesnumeric
BiPromoter rangesBidirectional-promoter sizes for ChIP region annotation. It's two values or a single value can be given. If a single value is given, it will be segmented into two equal fractions (e.g. 5000 is equivalent to 2500,5000) (--bisizes).5000promoter-bisizesstring
Relative distanceRelative distance to TSS/TTS in WIGGLE file profiling (--rel-dist).3000relative-distancestring
Gene group filesGene groups of particular interest in wig profiling. Each gene group file must have gene names in the 1st column. The file names are separated by commas (--gn-groups).
Gene group namesSet this parameter empty for using default values. The names of the gene groups from "Gene group files" parameter. These names appear in the legends of the wig profiling plots. Values range: comma-separated list of strings. Default value: 'Group 1, Group 2,...Group n' (--gn-group-names).

Input/Output Ports

The element has 1 input port:

Name in GUI: CEAS data

Name in Workflow File: in-data


Slot In GUISlot in Workflow FileType
Enrichment signalenrichment-signalann-table-list
Peak regionspeak-regionsstring
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