kallisto_index: Index the transcriptome for kallisto

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

Index the transcriptome for kallisto

Description

Index the transcriptome for kallisto

Usage

kallisto_index(
  kallistoindex = "results/05_quantification/kallisto/idx",
  transcriptome_path = NULL
)

Arguments

kallistoindex	Directory where kallisto index file will be stored. Default: results/05_quantification/kallisto/idx.
transcriptome_path	Path to the reference transcriptome FASTA file.

Value

A 2-column data frame with path to index file 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

kallistoindex <- file.path(tempdir(), "idx")
transcriptome_path <- system.file(
     "extdata", "Hsapiens_GRCh37.75_subset_transcripts.fa", package="bears"
)
if(kallisto_is_installed()) {
    kallisto_index(kallistoindex, transcriptome_path)
}

almeidasilvaf/bears documentation built on April 14, 2023, 7:06 p.m.