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
in GUI| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output directory | Directory to save MACS output files. | out-dir |
string | |
| Reference annotation | Merge the input assemblies together with this reference annotation. |
| ref-annotation | string | ||
| Reference sequence | The 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-seq |
| string | ||||
| Minimum isoform fraction | Discard isoforms with abundance below this. | 0.05 | min-isoform-fraction | numeric |
| Cuffcompare tool path | The path to the Cuffcompare external tool in UGENE. | default | cuffcompare-tool-path | string |
| Cuffmerge tool path | The path to the Cuffmerge external tool in UGENE. | default | path | string |
| Temporary directory | The directory for temporary files. | default |
Parameters in Workflow File
Type: cuffmerge
Parameterout-dir Output directory ref-annotation Reference annotation string ref-seq Reference sequence string min-isoform-fraction Minimum isoform fraction numeric cuffcompare-tool-path Cuffcompare tool path string path Cuffmerge tool path string
Parameter in the GUI Type
Temporary directory
string
| tmp-dir |
| string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Set of annotations
Name in Workflow File: in-assembly
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | in-annotations | ann_table |
And 1 output port:
Name in GUI: Set of annotations
Name in Workflow File: out-assembly
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Set of annotations | out-annotations | ann_table |