sc_atac_create_fragments: Generating the popular fragments for scATAC-Seq data

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

Generating the popular fragments for scATAC-Seq data

Description

Takes in a tagged and sorted BAM file and outputs the associated fragments in a .bed file

Usage

sc_atac_create_fragments(
  inbam,
  output_folder = "",
  min_mapq = 30,
  nproc = 1,
  cellbarcode = "CB",
  chromosomes = "^chr",
  readname_barcode = NULL,
  cells = NULL,
  max_distance = 5000,
  min_distance = 10,
  chunksize = 5e+05
)

Arguments

inbam	The tagged, sorted and duplicate-free input BAM file
output_folder	The path of the output folder
min_mapq	: int Minimum MAPQ to retain fragment
nproc	: int, optional Number of processors to use. Default is 1.
cellbarcode	: str Tag used for cell barcode. Default is CB (used by cellranger)
chromosomes	: str, optional Regular expression used to match chromosome names to include in the output file. Default is "(?i)^chr" (starts with "chr", case-insensitive). If None, use all chromosomes in the BAM file.
readname_barcode	: str, optional Regular expression used to match cell barocde stored in read name. If None (default), use read tags instead. Use "[^:]*" to match all characters before the first colon (":").
cells	: str File containing list of cell barcodes to retain. If None (default), use all cell barcodes found in the BAM file.
max_distance	: int, optional Maximum distance between integration sites for the fragment to be retained. Allows filtering of implausible fragments that likely result from incorrect mapping positions. Default is 5000 bp.
min_distance	: int, optional Minimum distance between integration sites for the fragment to be retained. Allows filtering implausible fragments that likely result from incorrect mapping positions. Default is 10 bp.
chunksize	: int Number of BAM entries to read through before collapsing and writing fragments to disk. Higher chunksize will use more memory but will be faster.

Value

returns NULL

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