# 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

## gencode_transcripts

# 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
recipeLoad('gencode_transcripts', return = TRUE)
gencode_transcripts$species <- 'mouse'
gencode_transcripts$version <- 'M31'
getData(gencode_transcripts, outdir = 'data/folder', notes = 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')