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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.

Parameters in GUI

ParameterDescriptionDefault value
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).hg19
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).3000
Wiggle profiling resolutionWiggle profiling resolution. WARNING: Value smaller than the wig interval (resolution) may cause aliasing error. (--pf-res).50
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).3000
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).5000
Relative distanceRelative distance to TSS/TTS in WIGGLE file profiling (--rel-dist).3000
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). 

Parameters in Workflow File

Type: ceas-report

ParameterParameter in the GUIType
image-fileOutput report file

string

anns-fileOutput annotations filestring
anns-tableGene annotations tablestring
spanSpan sizenumeric
profiling-resolutionWiggle profiling resolutionnumeric
promoter-sizesPromoter/downstream intervalnumeric
promoter-bisizesBiPromoter rangesstring
relative-distanceRelative distancestring
group-filesGene group filesstring
group-namesGene group namesstring

Input/Output Ports

The element has 1 input port:

Name in GUI: CEAS data

Name in Workflow File: in-data

Slots:

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