gen_cellecta_bc_data: Extract cellecta barcode information from a sam or bam file

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Extract cellecta barcode information from a sam or bam file

Description

Extract cellecta barcode information from a sam or bam file

Usage

gen_cellecta_bc_data(
  file,
  verbose = FALSE,
  output = tempfile(),
  samtools_module = FALSE
)

Arguments

file	Input sam or bam file
verbose	Optional updates during parsing
output	File to write out
samtools_module	For slurm, which modules to load

Details

For some reason, this function does not cancel when ordered. Either kill the R session or kill the process directly on the server

Value

A tibble of the cell ids and lineage tracing barcodes

Examples

## Not run: 
cid_lt <- gen_cellecta_bc_data(file = "path/to/file.bam",
                               verbose = TRUE,
                               samtools_module = "GCC/9.3.0 SAMtools/1.10")

cid_lt <- gen_cellecta_bc_data(
   file = "/home/gdrobertslab/lab/Counts/S0027/outs/S0016-S0027-bc2.sam",
   verbose = TRUE,
   samtools_module = "GCC/9.3.0 SAMtools/1.10")

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.