Perform transcript quantification using Salmon's selective-alignment-based mode from raw RNA-seq reads.
Usage
salmon_quant(
input_r1,
input_r2 = NULL,
index_path = "salmon_index",
output_dir = "quant_output",
num_threads = 8,
num_gibbs = 100,
min_score_fraction = "0.65",
env_name = "salmon-env"
)Arguments
- input_r1
Path to the FASTQ file for read 1 (or single-end reads).
- input_r2
Optional path to the FASTQ file for read 2 (paired-end reads).
- index_path
Path to the Salmon index directory (default is "salmon_index").
- output_dir
Directory to save the quantification output (default is "quant_output").
- num_threads
Number of threads to use (default is 8).
- num_gibbs
Number of Gibbs samples for uncertainty estimation (default is 100).
- min_score_fraction
Minimum score fraction for alignments (default is "0.65").
- env_name
Name of the conda environment with Salmon installed (default is "salmon-env").