sc_exon_mapping: sc_exon_mapping

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

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

The function can accept multiple bam file as input, if multiple bam file is provided and the 'bc_len' is zero, then the function will use the barcode in the 'barcode_vector' to insert into the 'bc' bam tag. So the length of 'barcode_vector' and the length of 'inbam' should be the same If this is the case then the 'max_mis' argument in 'sc_demultiplex' should be zero. If 'be_len' is larger than zero, then the function will still seek for barcode in fastq headers with given length. In this case each bam file is not treated as from a single cell.

Usage

sc_exon_mapping(
  inbam,
  outbam,
  annofn,
  bam_tags = list(am = "YE", ge = "GE", bc = "BC", mb = "OX"),
  bc_len = 8,
  barcode_vector = "",
  UMI_len = 6,
  stnd = TRUE,
  fix_chr = FALSE,
  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
barcode_vector	a list of barcode if each individual bam is a single cell. (default: NULL). The barcode should be of the same length for each cell.
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)
nthreads	number of threads to use. (default: 1)

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)

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