align_based_quan: alignment-based workflow

In sunshanwen/BP4RNAseq: A babysitter's package for reproducible RNA-seq analysis

alignment-based workflow

Description

alignment-based workflow

Usage

align_based_quan(
  pair,
  taxa,
  genome,
  annotation,
  novel_transcript = FALSE,
  threads = 4,
  hisat2_build_add = NULL,
  hisat2_add = NULL,
  stringtie_add = NULL
)

Arguments

pair	'single' for single-end (SE) or 'paired' for paired-end (PE) reads.
taxa	the scientific or common name of the organism.
genome	the reference genome.
annotation	the annotation file.
novel_transcript	logic, whether identifying novel transcripts is expected or not. Default is FALSE.
threads	the number of threads to be used. Default is 4.
hisat2_build_add	additional parameters to customize hisat2 build command. Default is NULL.
hisat2_add	additional parameters to customize hisat2 command. Default is NULL.
stringtie_add	additional parameters to customize stringtie command. Default is NULL.

Value

None

Examples

## Not run: 
test_Homo_sapiens.fna <- system.file('extdata', 'test_Homo_sapiens.fna', package = 'BP4RNAseq')
test_Homo_sapiens.gff <- system.file('extdata', 'test_Homo_sapiens.gff', package = 'BP4RNAseq')
align_based_quan(pair = 'paired', taxa = 'Homo sapiens', 
genome = test_Homo_sapiens.fna, 
annotation = test_Homo_sapiens.gff, novel_transcript = FALSE)

## End(Not run)

sunshanwen/BP4RNAseq documentation built on March 28, 2022, 5:35 p.m.