# ensembl_liftover
Download and unzip genome liftover file from Ensembl
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/ensembl_liftover.R (opens new window)
Data source: https://ftp.ensembl.org/pub/assembly_mapping/ (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| species | species | string | 'human' or 'mouse', which maps to the 'homo_sapiens' or 'mus_musculus' folder under source URL |
| from | from | string | original genome build (case sensitive, must match source URL) |
| to | to | string | target genome build (case sensitive, must match source URL) |
# Outputs
| label | type | description | |
|---|---|---|---|
| liftover | liftover | File[] | the unzipped liftover file: ${from}_to_${to}.chain |
# Example:
## Get data from evaluting recipe
ensembl_liftover <- recipeLoad('ensembl_liftover')
ensembl_liftover$species <- 'human'
ensembl_liftover$from <- 'GRCh37'
ensembl_liftover$to <- 'GRCh38'
getData(ensembl_liftover, outdir = 'data/folder', notes = c('grch37', 'grch38'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('ensembl', 'GRCh37'))
## Get data from Google bucket directly
dataUpdate('data/folder', cloud=TRUE)
dh <- dataSearch(c('ensembl', 'GRCh37'))
getCloudData(dh[1], outdir = 'data/folder')