sc_demultiplex_and_count {scPipe} | R Documentation

## 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 consistant 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)

[Package scPipe version 1.8.0 Index]