Page tree
Skip to end of metadata
Go to start of metadata

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

Parameters

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

string

Reference annotationMerge the input assemblies together with this reference annotation.
ref-annotationstring
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.
ref-seqstring
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

Slots:

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

Slots:

Slot In GUISlot in Workflow FileType
Set of annotationsout-annotationsann_table
  • No labels