Run cellranger

Run cellranger

Usage

cellranger(subcmd = NULL, ..., cellranger = NULL)

Arguments

subcmd

Sub-Command of cellranger.

...

<dynamic dots> Additional arguments passed to cellranger command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote(). Details see: cmd_help(cellranger()).

cellranger

A string of path to cellranger command.

Value

A command object.

See also

• https://github.com/10XGenomics/cellranger

• https://www.10xgenomics.com/support/software/cell-ranger/latest

• https://www.10xgenomics.com/support/software/cell-ranger/downloads#reference-downloads

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Other commands: allele_counter(), bcftools(), bedtools(), bowtie2(), bwa(), conda(), fastp(), fastq_pair(), gistic2(), kraken2(), kraken_tools(), perl(), pyscenic(), python(), samtools(), seqkit(), snpEff(), trust4(), varscan()

Examples

if (FALSE) { # \dontrun{
fastq_dir  # 10x raw fastq files directory
genome_ref # Please download the transcriptome reference data
cellranger(
    "count",
    sprintf("--fastqs=%s", fastq_dir),
    sprintf("--id=%s", basename(fastq_dir)),
    sprintf("--sample=%s", basename(fastq_dir)),
    sprintf("--localcores=%s", parallel::detectCores()),
    sprintf("--transcriptome=%s", genome_ref),
    sprintf("--chemistry=%s", shQuote("auto")),
    "--nosecondary"
)
} # }