sc_demultiplex: sc_demultiplex

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

sc_demultiplex

Description

Process bam file by cell barcode, output to outdir/count/[cell_id].csv. the output contains information for all reads that can be mapped to exons. including the gene id, UMI of that read and the distance to transcript end position.

Usage

sc_demultiplex(
  inbam,
  outdir,
  bc_anno,
  max_mis = 1,
  bam_tags = list(am = "YE", ge = "GE", bc = "BC", mb = "OX"),
  mito = "MT",
  has_UMI = TRUE,
  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)
nthreads	number of threads to use. (default: 1)

Value

no return

Examples

data_dir="celseq2_demo"
barcode_annotation_fn = system.file("extdata", "barcode_anno.csv",
    package = "scPipe")
## Not run: 
# refer to the vignettes for the complete workflow
...
sc_demultiplex(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.