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)
}