sc_count_aligned_bam {scPipe} | R Documentation

## sc_count_aligned_bam

### Description

Wrapper to run `sc_exon_mapping`, `sc_demultiplex` and `sc_gene_counting` with a single command

### Usage

    sc_count_aligned_bam(inbam, outbam, annofn, bam_tags = list(am = "YE", ge =
      "GE", bc = "BC", mb = "OX"), bc_len = 8, UMI_len = 6, stnd = TRUE,
      fix_chr = FALSE, outdir, bc_anno, max_mis = 1, mito = "MT",
      has_UMI = TRUE, UMI_cor = 1, gene_fl = FALSE, keep_mapped_bam = TRUE,
      nthreads = 1)

### Arguments

`inbam` | input aligned bam file. can have multiple files as input
`outbam` | output bam filename
`annofn` | single string or vector of gff3 annotation filenames, data.frame in SAF format or GRanges object containing complete gene_id metadata column.
`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
`bc_len` | total barcode length
`UMI_len` | UMI length
`stnd` | TRUE to perform strand specific mapping. (default: TRUE)
`fix_chr` | TRUE to add 'chr' to chromosome names, MT to chrM. (default: FALSE)
`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)
`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.
`keep_mapped_bam` | TRUE if feature mapped bam file should be retained.
`nthreads` | number of threads to use. (default: 1)

### Value

no return

### Examples

    ## Not run:
    sc_count_aligned_bam(
      inbam = "aligned.bam",
      outbam = "mapped.bam",
      annofn = c("MusMusculus-GRCm38p4-UCSC.gff3", "ERCC92_anno.gff3"),
      outdir = "output",
      bc_anno = "barcodes.csv"
    )

    ## End(Not run)

[Package scPipe version 1.9.4 Index]