# ucsc_database
UCSC genome annotation database from UCSC golden path
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/ucsc_database.R (opens new window)
Data source: https://hgdownload.soe.ucsc.edu/downloads.html (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| build | build | string | genome build version, e.g. 'hg19', 'hg38', 'mm39' |
| dbname | dbname | string | genome annotation database name, e.g. 'refGene', 'knownGene' |
# Outputs
| label | type | description | |
|---|---|---|---|
| database | database | File[] | the unzipped annotation txt file and sql script |
# Example:
## Get data from evaluting recipe
ucsc_database <- recipeLoad('ucsc_database')
ucsc_database$build <- 'hg38'
ucsc_database$dbname <- 'refGene'
getData(ucsc_database, outdir = 'data/folder', notes = c('ucsc', 'annotation', 'database', 'hg38', 'refGene'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('ucsc', 'annotation', 'database', 'hg38', 'refGene'))