sc_aligning: aligning the demultiplexed FASTQ reads using the...

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

aligning the demultiplexed FASTQ reads using the Rsubread:align()

Description

after we run the sc_trim_barcode or sc_atac_trim_barcode to demultiplex the fastq files, we are using this function to align those fastq files to a known reference.

Usage

sc_aligning(
  R1,
  R2 = NULL,
  tech = "atac",
  index_path = NULL,
  ref = NULL,
  output_folder = NULL,
  output_file = NULL,
  input_format = "FASTQ",
  output_format = "BAM",
  type = "dna",
  nthreads = 1
)

Arguments

R1	a mandatory character vector including names of files that include sequence reads to be aligned. For paired-end reads, this gives the list of files including first reads in each library. File format is FASTQ/FASTA by default.
R2	a character vector, the second fastq file, which is required if the data is paired-end
tech	a character string giving the sequencing technology. Possible value includes "atac" or "rna"
index_path	character string specifying the path/basename of the index files, if the Rsubread genome build is available
ref	a character string specifying the path to reference genome file (.fasta, .fa format)
output_folder	a character string, the name of the output folder
output_file	a character vector specifying names of output files. By default, names of output files are set as the file names provided in R1 added with an suffix string
input_format	a string indicating the input format
output_format	a string indicating the output format
type	type of sequencing data ('RNA' or 'DNA')
nthreads	numeric value giving the number of threads used for mapping.

Value

the file path of the output aligned BAM file

Examples

## Not run: 
sc_aligning(index_path,
    tech = 'atac',
    R1,  
    R2, 
    nthreads  = 6) 

## End(Not run)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.