fastq2quan: Produce the quantifications of gene expression based on the...

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

Produce the quantifications of gene expression based on the fastq files.

Description

Produce the quantifications of gene expression based on the fastq files with alignment-based and alignment-free workflows.

Usage

fastq2quan(
  threads = 4,
  dir = getwd(),
  pair,
  taxa,
  novel_transcript = FALSE,
  scRNA = FALSE,
  protocol = NULL
)

Arguments

threads	the number of threads to be used. Default is 4.
dir	the working directory. Default is the current working directory.
pair	'single' for single-end (SE) reads or 'paired' for paired-end (PE) reads.
taxa	the scientific or common name of the organism.
novel_transcript	logic, whether identifying novel transcripts is expected or not. Default is FALSE.
scRNA	logic, whether single-cell RNA-seq is quantified or not. Default is FALSE.
protocol	the single-cell RNA sequencing protocol: dropseq, chromium, or chromiumV3.

Value

None

Examples

sra_download(accession = 'SRR11427582')
sra2fastq()
fastq2quan(pair = 'single', taxa = 'Drosophila melanogaster')

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