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)
}