# 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

## STAR_index

# 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:

recipeLoad('STAR_index.R', return = TRUE)
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'))