sc_correct_bam_bc {scPipe} | R Documentation

## sc_correct_bam_bc

### Description

update the cell barcode tag in bam file with corrected barcode output to a new bam file. the function will be useful for methods that use the cell barcode information from bam file, such as 'Demuxlet'

### Usage

    sc_correct_bam_bc(inbam, outbam, bc_anno, max_mis = 1, bam_tags = list(am =
      "YE", ge = "GE", bc = "BC", mb = "OX"), mito = "MT", nthreads = 1)

### Arguments

`inbam` | input bam file. This should be the output of `sc_exon_mapping`
`outbam` | output bam file with updated cell barcode
`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.
`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_correct_bam_bc(file.path(data_dir, "out.map.bam"),
        file.path(data_dir, "out.map.clean.bam"),
        barcode_annotation_fn)
    ...

    ## End(Not run)

[Package scPipe version 1.9.4 Index]