# 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

## gencode_annotation

# 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')