sc_atac_bam_tagging: BAM tagging

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

BAM tagging

Description

Demultiplexes the reads

Usage

sc_atac_bam_tagging(
  inbam,
  output_folder = NULL,
  bc_length = NULL,
  bam_tags = list(bc = "CB", mb = "OX"),
  nthreads = 1
)

Arguments

inbam	The input BAM file
output_folder	The path of the output folder
bc_length	The length of the cellular barcodes
bam_tags	The BAM tags
nthreads	The number of threads

Details

sc_atac_bam_tagging()

Value

file path of the resultant demmultiplexed BAM file.

Examples

r1 <- system.file("extdata", "small_chr21_R1.fastq.gz", package="scPipe")
r2 <- system.file("extdata", "small_chr21_R3.fastq.gz", package="scPipe")
barcode_fastq <- system.file("extdata", "small_chr21_R2.fastq.gz", package="scPipe")
out <- tempdir()

sc_atac_trim_barcode(r1=r1, r2=r2, bc_file=barcode_fastq, output_folder=out)

demux_r1 <- file.path(out, "demux_completematch_small_chr21_R1.fastq.gz")
demux_r2 <- file.path(out, "demux_completematch_small_chr21_R3.fastq.gz")
reference <- system.file("extdata", "small_chr21.fa", package="scPipe")

aligned_bam <- sc_aligning(ref=reference, R1=demux_r1, R2=demux_r2, nthreads=6, output_folder=out)

out_bam <- sc_atac_bam_tagging(
   inbam = aligned_bam,
   output_folder = out,
   nthreads = 6)

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