# STAR_index
ultrafast universal RNA-seq and scRNAseq aligner
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/STAR_index.R (opens new window)
Data source: https://github.com/alexdobin/STAR (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| ref | reference genome | string;File | The reference genome file |
| gtf | GTF | string;File | gene annotation file |
| genomeDir | genomeDir | string | The directory for index files. |
| threads | threads | int | The number of threads to use |
| sjdb | sjdbOverhang | int | The length of the genomic sequence around the annotated junction |
# Outputs
| label | type | description | |
|---|---|---|---|
| idx | STAR index | Directory | The directory for STAR index files |
# Example:
STAR_index <- recipeLoad('STAR_index.R')
STAR_index$ref <- 'gcpData/reference_genome/GRCh38.primary_assembly.genome.fa'
STAR_index$gtf <- 'gcpData/gencode_annotation/gencode.v42.annotation.gtf'
STAR_index$sjdb <- 100
STAR_index$genomeDir <- 'GRCh38.GENCODE.v42_100'
STAR_index$threads <- 16
getData(STAR_index, outdir = 'gcpData', notes =c('STAR_index', 'GRCh38.primary_assembly', 'gencode.v42', 'star_2.7.9a'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('STAR_index', 'GRCh38.primary_assembly', 'gencode.v42', 'star_2.7.9a'))