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  • Annotate Peaks with peak2gene Element
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Gets refGenes near the ChIP regions identified by a peak-caller.

Parameters in GUI

ParameterDescriptionDefault value
Genome file Select a genome file (sqlite3 file) to search refGenes. (--genome).hg19
Output fileSelect which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down. (--op).all
Official gene symbolsOutput official gene symbol instead of refseq name. (--symbol).False
DistanceSet a number which unit is base. It will get the refGenes in n bases from peak center. (--distance).3000

Parameters in Workflow File

Type: peak2gene-id

ParameterParameter in the GUIType
genomeGenome file


outposOutput filestring
symbolOfficial gene symbolsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Peak2gene data

Name in Workflow File: in-data


Slot In GUISlot in Workflow FileType
Treatment features_treat-annann-table-list

And 1 output port:

Name in GUI: Peak2gene output data

Name in Workflow File: out-data


Slot In GUISlot in Workflow FileType
Gene regionsgene-annotationann-table-list
Peak regionspeak-annotationann-table-list
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