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  • Merge Assemblies with Cuffmerge Element

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Parameters in GUI

ParameterDescriptionDefault value
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.0.05
Cuffcompare tool pathThe path to the Cuffcompare external tool in UGENE.default
Cuffmerge tool pathThe path to the Cuffmerge external tool in UGENE.default
Temporary directoryThe directory for temporary files.default

Parameters in

Schema File

Workflow File

Type: cuffmerge

ParameterParameter in the GUIType
out-dirOutput directory

string

ref-annotationReference annotationstring
ref-seqReference sequencestring
min-isoform-fractionMinimum isoform fractionnumeric
cuffcompare-tool-pathCuffcompare tool pathstring
pathCuffmerge tool pathstring
tmp-dirTemporary directorystring

Input/Output Ports

The element has 1 input port:

Name in GUI: Set of annotations

Name in Schema File Workflow File: in-assembly

Slots:

Slot In GUISlot in Schema Workflow FileType
Set of annotationsin-annotationsann_table

And 1 output port:

Name in GUI: Set of annotations

Name in Schema File Workflow File: out-assembly

Slots:

Slot In GUISlot in Schema Workflow FileType
Set of annotationsout-annotationsann_table