sc_count_aligned_bam: sc_count_aligned_bam

Description Usage Arguments Value Examples

View source: R/wrapper_scPipeCPP.R

Description

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

Usage

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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

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## 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)

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.