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 1.4.1 Index]