BLAZE Assign reads to cell barcodes.

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

Usage

blaze(expect_cells, fq_in, ...)

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
...: Additional BLAZE configuration parameters. E.g., setting `'output-prefix'='some_prefix'` is equivalent to specifying `–output-prefix some_prefix` in BLAZE; Similarly, `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,
  "output-prefix" = file.path(outdir, ""),
  "output-fastq" = file.path(outdir, "output.fastq"),
  overwrite=TRUE
)
#> $`output-prefix`
#> [1] "/tmp/RtmpgpEV0i/file25bf762f8697/"
#> 
#> $`output-fastq`
#> [1] "/tmp/RtmpgpEV0i/file25bf762f8697/output.fastq"
#> 
#> $overwrite
#> [1] TRUE
#> 
#> Running BLAZE...
#> Argument:  --expect-cells  10 --overwrite --minimal_stdout  --output-prefix /tmp/RtmpgpEV0i/file25bf762f8697/ --output-fastq /tmp/RtmpgpEV0i/file25bf762f8697/output.fastq /__w/_temp/Library/FLAMES/extdata/fastq/musc_rps24.fastq.gz