sc_demultiplex {scPipe}R Documentation

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 consistant 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)


[Package scPipe version 1.8.0 Index]