# gencode_transcripts
Download, unzip, and index transcripts files from gencode
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/gencode_transcripts.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 | |
|---|---|---|---|
| transcripts | transcripts | File[] | the samtool indexed annotation files: *transcripts.fa, *transcripts.fa.fai |
# Example:
## Get data from evaluating recipe
gencode_transcripts <- recipeLoad('gencode_transcripts')
gencode_transcripts$species <- 'mouse'
gencode_transcripts$version <- 'M31'
getData(gencode_transcripts, outdir = 'data/folder', notes = c('gencode', 'transcripts', 'mouse', 'M31'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('gencode', 'transcripts', 'mouse', 'M31'))
## Get data from Google bucket directly
dataUpdate('data/folder', cloud=TRUE)
dh <- dataSearch(c('gencode', 'transcripts'))
getCloudData(dh[1], outdir = 'data/folder')