run.salmon: Run Salmon

In FemeniasM/ExplorATEproject: Explore Active Transposable Elements from RNAseq data

Run Salmon

Description

This function helps the user to run the Salmon program. The user must assign the location of the program, an output directory, the transcriptome, the location of the libraries, the kmer size, the processing threads, and a label for the index.

Usage

run.salmon(
  index,
  decoys,
  salmon_path = "salmon",
  kmer,
  lib_dir,
  pe_se = c("pe", "se"),
  threads,
  trme
)

Arguments

index	paterrn of output salmon directory. This tag will be used to create the index and a folder containing the counts for each library
decoys	The location path of the decoy.txt file generated by the mk.reference function
salmon_path	A path indicating the location of the program
kmer	The kmer size used during Salmon indexing
lib_dir	A path indicating the location of libraries. Libraries should be tagged with ".fastq.gz" (single-end) or "_R#.fastq.gz" (paired-end) at the end, for example: anyName.fastq.gz (single-end) or anyName_R1.fastq.gz and anyName_R2.fastq.gz (paired-end)
pe_se	Indicate if you using paired-end ("pe") or single-end ("se") libraries
threads	number of threads to be used
trme	A path indicating the location of transcriptome
output_dir	output salmon directory

FemeniasM/ExplorATEproject documentation built on Nov. 30, 2022, 5:26 p.m.