salmon_index_transcriptome: salmon_index_transcriptome

In jrboyd/ssvRecipes: Recipes using seqsetvis

salmon_index_transcriptome

Description

creates the salmon index for transcriptome created from specified assembly fasta and gene reference gtf.

Usage

salmon_index_transcriptome(
  seq_path = HG38_SEQ_PATH,
  gtf_path = HG38_v28_GTF_URL,
  gtf_to_fasta_path = GTF_TO_FASTA_PATH,
  salmon_path = SALMON_PATH,
  output_transcriptome = NULL,
  output_index = NULL,
  cache_path = "~/.cache",
  use_qsub = TRUE,
  do_submit = TRUE
)

Arguments

seq_path	path to local file or url to assembly fasta (only tested with hg38).
gtf_path	path to local file or url to gtf reference (only tested with gencode hg38 v28 gtf).
gtf_to_fasta_path	local path to tophat2 gtf_to_fasta utility.
salmon_path	path to main salmon executable.
output_transcriptome	file path for transcriptome output.
output_index	file path for index for transcriptome.
cache_path	path to cache directory, will be created if necessary.
use_qsub	whether to qsub a script. if FALSE will use a direct system command
do_submit	if FALSE, will not perform qsub.

Value

list containing path to index and job_id if relevant

Examples

# as this may download several gigs of data, do not run
## Not run: 
salmon_index_transcriptome()

## End(Not run)

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.