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)

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)

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.

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.

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 1.2.1 Index]