Create a Salmon index from a reference transcriptome FASTA file.
Usage
salmon_index(
fasta_path,
index_path = "salmon_index",
kmer_len = 31,
num_threads = 2,
env_name = "salmon-env",
is_gencode = FALSE,
decoy_fasta = NULL,
clip_poly_a = TRUE
)Arguments
- fasta_path
Path to the reference transcriptome FASTA file.
- index_path
Directory path to save the Salmon index (default is "salmon_index").
- kmer_len
K-mer length for the index (default is 31).
- num_threads
Number of threads to use (default is 2).
- env_name
Name of the conda environment with Salmon installed (default is "salmon-env").
- is_gencode
Logical indicating if the FASTA is from GENCODE (default is
FALSE).- decoy_fasta
Optional path to a FASTA file containing decoy sequences (default is
NULL).- clip_poly_a
Logical indicating whether to clip poly-A tails (default is
TRUE).