# gencode_annotation
Download and unzip annotation files from gencode
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/gencode_annotation.R (opens new window)
Data source: http://ftp.ebi.ac.uk/pub/databases/gencode/ (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| species | species | string | 'human' or 'mouse' |
| version | version | string | Character string. Case sensitive. must match available versions for each species under source URL link. e.g., 'M31' (species='mouse'), '42' (species='human') |
# Outputs
| label | type | description | |
|---|---|---|---|
| annotation | annotation | File[] | the unzipped annotation file: gencode.v$version.annotation.gtf |
# Example:
## Get data from evaluting recipe
recipeLoad('gencode_annotation', return = TRUE)
gencode_annotation$species <- 'human'
gencode_annotation$version <- '42'
getData(gencode_annotation, outdir = 'data/folder', notes = c('gencode', 'annotation', 'human', '42'))
## Get data from Google bucket directly
dataUpdate('data/folder', cloud=TRUE)
dh <- dataSearch(c('gencode', 'annotation'))
getCloudData(dh[1], outdir = 'data/folder')