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 1.0.6 Index]