sc_exon_mapping {scPipe} | R Documentation

## sc_exon_mapping

### Description

Map aligned reads to exon annotation. The result will be written into optional fields in bam file with different tags. Following this link for more information regarding to bam file format: http://samtools.github.io/hts-specs

### Usage

    sc_exon_mapping(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)

### Arguments

`inbam` | input aligned bam file
`outbam` | output bam filename
`annofn` | single string or vector of gff3 annotation filenames
`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)

### Value

generates a bam file with exons assigned

### Examples

    data_dir="celseq2_demo"
    ERCCanno_fn = system.file("extdata", "ERCC92_anno.gff3",
        package = "scPipe")
    ## Not run:
    # for the complete workflow, refer to the vignettes
    ...
    sc_exon_mapping(file.path(data_dir, "out.aln.bam"),
                    file.path(data_dir, "out.map.bam"),
                    ERCCanno_fn)
    ...

    ## End(Not run)

[Package scPipe version 1.2.1 Index]