star_align_fastq_PE | R Documentation |
Title
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 )
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. |
list length 2 of output dirs and job ids
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.