Up: Component summary Component

LiftOver

Converts 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

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