star_align_fastq_PE: Title

In jrboyd/ssvRecipes: Recipes using seqsetvis

Title

Description

Title

Usage

star_align_fastq_PE(
  r1_fastq_paths,
  r2_fastq_paths = NULL,
  pair_key = "P",
  r1_to_r2_FUN = function(r1) {     sub(paste0(pair_key, "1.fastq"), paste0(pair_key,
    "2.fastq"), r1) },
  index_path = HG38_STAR_INDEX,
  gtf_path = HG38_v28_GTF_URL,
  star_path = STAR_PATH,
  cache_path = "~/.cache",
  n_cores = 8,
  hold_jids = NA,
  out_path = file.path(getwd(), "alignment"),
  output_prefix = paste0(sub(paste0("_", pair_key, "1.fastq"), "",
    basename(r1_fastq_paths)), ".STAR."),
  do_submit = TRUE
)

Arguments

r1_fastq_paths	paths to r1 files, mandatory
r2_fastq_paths	paths to r2 files, will try to derive by calling r1_to_r2_FUN(r1_fastq_paths)
r1_to_r2_FUN	optional function if r2 files no supplied
gtf_path	path (local or url) to gtf
star_path	path to star executable
cache_path	cache location
n_cores	number of threads to use
hold_jids	job ids to hold for, default NA is none.
out_path	directory to output to
output_prefix	custom output directory per fastq_paths. default is basename of fastq_paths
do_submit	if FALSE, qsub is skipped but submit scripts remain. Default is TRUE.

Value

list length 2 of output dirs and job ids

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