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Cuffmerge merges together several assemblies. It also handles running Cuffcompare for you and automatically filters a number of transfrags that are probably artifacts. If you have a reference file available, you can provide it to Cuffmerge in order to gracefully merge input (e.g. novel) isoforms and known isoforms and maximize overall assembly quality.

Element type: cuffmerge


ParameterDescriptionDefault valueParameter in Workflow FileType
Output directoryDirectory to save MACS output files.


Reference annotationMerge the input assemblies together with this reference annotation.
Reference sequenceThe genomic DNA sequences for the reference. It is used to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, transcripts consisting mostly of lower-case bases are classified as repeats.
Minimum isoform fractionDiscard isoforms with abundance below this.0.05min-isoform-fractionnumeric
Cuffcompare tool pathThe path to the Cuffcompare external tool in UGENE.defaultcuffcompare-tool-pathstring
Cuffmerge tool pathThe path to the Cuffmerge external tool in UGENE.defaultpathstring
Temporary directoryThe directory for temporary files.defaulttmp-dirstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Set of annotations

Name in Workflow File: in-assembly


Slot In GUISlot in Workflow FileType
Set of annotationsin-annotationsann_table

And 1 output port:

Name in GUI: Set of annotations

Name in Workflow File: out-assembly


Slot In GUISlot in Workflow FileType
Set of annotationsout-annotationsann_table
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