Up: Component summary
Up: Component summary
Component
LiftOverConverts chromosome region coordinates from one genome build to another. This component is a wrapper for UCSC LiftOver application.
| Version | 1.1 |
|---|---|
| Bundle | microarray |
| Categories | Analysis |
| Authors | Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | LiftOver |
| Source files | component.xml LiftOverRunner.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| regions | CSV | Mandatory | Original sequence locations of interest |
| chain | TextFile | Mandatory | LiftOver chain file that contains the mapping. |
Outputs| Name | Type | Description |
|---|---|---|
| out | CSV | A set of motifs that were found |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| colChr | string | "chr" | Column name for the chromosome name |
| colEnd | string | "end" | Column name for the end locus |
| colId | string | "id" | Column name for the sequence identifier |
| colStart | string | "start" | Column name for the start locus |
| command | string | "liftOver" | Name of LiftOver executable |
| minLength | int | 1 | Minimum sequence length that is accepted |
| multiple | boolean | true | Allow multiple output regions for each sequence |
Test cases| Test case | Parameters▼ | IN regions |
IN chain |
OUT out |
|---|---|---|---|---|
| case1 | (missing) | regions | chain | out |