sc_count_aligned_bam: sc_count_aligned_bam

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

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 consistent 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)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.