BLAZE Assign reads to cell barcodes.

Uses BLAZE to generate barcode list and assign reads to cell barcodes.

Usage

blaze(
  expect_cells,
  fq_in,
  outdir,
  fq_out,
  sample_name = "",
  additional_args = NULL,
  ...
)

Arguments

expect_cells

Integer, expected number of cells. Note: this could be just a rough estimate. E.g., the targeted number of cells.

fq_in

File path to the fastq file used as a query sequence file

outdir

Output directory to save BLAZE results.

fq_out

File path to save the output fastq file containing reads assigned to cell barcodes.

sample_name

Sample name prefix for output files. Default is an empty string.

additional_args

Additional command line style arguments to be passed to BLAZE. E.g. c("–10x-kit-version", "3v3")

...

Additional BLAZE configuration parameters. E.g., setting `overwrite=TRUE` is equivalent to switch on the `–overwrite` option. Note that the specified parameters will override the parameters specified in the configuration file. All available options can be found at https://github.com/shimlab/BLAZE.

Value

A data.frame summarising the reads aligned. Other outputs are written to disk. The details of the output files can be found at https://github.com/shimlab/BLAZE.

Examples

outdir <- tempfile()
dir.create(outdir)
fastq <- system.file("extdata", "fastq", "musc_rps24.fastq.gz", package = "FLAMES")
blaze(
  expect_cells = 10, fastq,
  outdir = outdir,
  fq_out = file.path(outdir, "blaze_matched_reads.fastq.gz"),
  overwrite = TRUE
)
#> $overwrite
#> [1] TRUE
#> 
#> Running BLAZE...
#> Argument:  --expect-cells  10 --output-prefix  /tmp/Rtmp4nGYdi/filebc4417549c72/ --output-fastq  matched_reads.fastq.gz --overwrite --minimal_stdout   /__w/_temp/Library/FLAMES/extdata/fastq/musc_rps24.fastq.gz 
#> NULL