Element name and description
Name of the element: "StringTie Gene Abundance Report"
Description of the element on the Scene: "Create a general report for several StringTie gene abundance output files."
Description of the element in the Property Editor:
The element summarizes gene abundance output of StringTie and saves the result into a common tab-delimited text file. The first two columns of the file are "Gene ID" and "Gene name". Each other column contains "FPKM" values for the genes from an input gene abundance file. Provide URL(s) to the StringTie gene abundance file(s) to the input port of the element.
Input data
There is one input port.
| Item | Value |
|---|---|
| Port name in GUI | Input StringTie gene abundance file(s) |
| Port description | URL(s) to sorted gene abundance file(s), produced by StringTie. |
| Port ID in UWL | in |
| Number of slots | 1 |
| Slot #1 name in GUI | Input URL |
| Slot #1 ID in UWL | url |
| Slot #1 data type | String |
Output data
There are no output ports.
Parameters
| # | Parameter | Description | Value in GUI | Default value |
|---|---|---|---|---|
| 1 | Output file | Specify the name of the output tab-delimited text file. | A line edit with the browse button nearby that opens a file browse dialog. | "StringTie_report.txt" |
Behavior
- The element should generate the common list of gene IDs and gene names and create the text file.
- The gene abundance columns should have a header that correspond to the input file names (suffix "_gene_abund.tab" should be cropped, if present).
- There should be "n/a" value, if a value for a gene is not available in a gene abundance file.
- The values should be sorted by "Gene ID".
- The result text file should be saved into the workflow output folder by default.
- blocks
-
UGENE-6155 Add "RNA-Seq analysis with TopHat and StringTie" sample workflow
-
- Closed
-