Gets refGenes near the ChIP regions identified by a peak-caller.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Genome file | Select a genome file (sqlite3 file) to search refGenes. (--genome). | hg19 |
| Output file | Select which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down. (--op). | all |
| Official gene symbols | Output official gene symbol instead of refseq name. (--symbol). | False |
| Distance | Set a number which unit is base. It will get the refGenes in n bases from peak center. (--distance). | 3000 |
Parameters in Workflow File
Type: peak2gene-id
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| genome | Genome file | string |
| outpos | Output file | string |
| symbol | Official gene symbols | boolean |
| distance | Distance | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Peak2gene data
Name in Workflow File: in-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Treatment features | _treat-ann | ann-table-list |
And 1 output port:
Name in GUI: Peak2gene output data
Name in Workflow File: out-data
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Gene regions | gene-annotation | ann-table-list |
| Peak regions | peak-annotation | ann-table-list |