salmon_index: Index the transcriptome for salmon

In almeidasilvaf/gead: Building Expression Atlas from RNA-Seq data

Index the transcriptome for salmon

Description

Index the transcriptome for salmon

Usage

salmon_index(
  salmonindex = "results/05_quantification/salmon/idx",
  transcriptome_path = NULL,
  klen = 31
)

Arguments

salmonindex	Directory where the transcriptome index will be stored. Default: results/05_quantification/salmon/idx.
transcriptome_path	Path to the reference transcriptome FASTA file.
klen	K-mer length. Default: 31.

Value

A 2-column data frame with path to index in the first column and index build status in the second column, with "OK" if the transcriptome index was successfully created, and NA otherwise.

Examples

salmonindex <- tempdir()
transcriptome_path <- system.file(
    "extdata", "Homo_sapiens.GRCh37.75_subset_transcripts.fa.gz", 
    package = "bears"
)
if(salmon_is_installed()) {
    salmon_index(salmonindex, transcriptome_path)
}

almeidasilvaf/gead documentation built on April 26, 2023, 3:47 p.m.