sc_demultiplex_and_count: sc_demultiplex_and_count

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

sc_demultiplex_and_count

Description

Wrapper to run sc_demultiplex and sc_gene_counting with a single command

Usage

sc_demultiplex_and_count(
  inbam,
  outdir,
  bc_anno,
  max_mis = 1,
  bam_tags = list(am = "YE", ge = "GE", bc = "BC", mb = "OX"),
  mito = "MT",
  has_UMI = TRUE,
  UMI_cor = 1,
  gene_fl = FALSE,
  nthreads = 1
)

Arguments

inbam	input bam file. This should be the output of sc_exon_mapping
outdir	output folder
bc_anno	barcode annotation, first column is cell id, second column is cell barcode sequence
max_mis	maximum mismatch allowed in barcode. (default: 1)
bam_tags	list defining BAM tags where mapping information is stored. "am": mapping status tag "ge": gene id "bc": cell barcode tag "mb": molecular barcode tag
mito	mitochondrial chromosome name. This should be consistent with the chromosome names in the bam file.
has_UMI	whether the protocol contains UMI (default: TRUE)
UMI_cor	correct UMI sequencing error: 0 means no correction, 1 means simple correction and merge UMI with distance 1. 2 means merge on both UMI alignment position match.
gene_fl	whether to remove low abundance genes. A gene is considered to have low abundance if only one copy of one UMI is associated with it.
nthreads	number of threads to use. (default: 1)

Value

no return

Examples

## Not run: 
refer to the vignettes for the complete workflow, replace demultiplex and
count with single command:
...
sc_demultiplex_and_count(
   file.path(data_dir, "out.map.bam"),
   data_dir,
   barcode_annotation_fn,
   has_UMI = FALSE
)
...

## End(Not run)

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