cellranger_count: Estimate scRNAseq Gene Expression with Cellranger Count
In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description Usage Arguments Details See Also

Perform mapping, cell estimation, filtering and gene expression analysis using the Cellranger software.

cellranger_count(
  id,
  fastqdir,
  refdir,
  outdir = ".",
  chemistry = "auto",
  nthreads = 4,
  sample = NULL,
  remake = FALSE
)

`id`	an id that identifies the sample, this will be embedded in the read-groups (`RG` tag) of the header and reads of the bam-file.
`fastqdir`	a dir with fastq files prepared with bamtofastq
`refdir`	a directory with the reference files created by the cellranger_mkref
`outdir`	a non-existing output directory, see details
`chemistry`	optional a 10X chemistry, use only when the autodetection is failing
`nthreads`	optional a number of threads to run on
`sample`	optional a file prefix to specify which sample to select, required if fastqdir contains fastq files for multiple samples
`remake`	optional remake the output if it already exists

To mark a succesful run, the function creates a completed status file in the output directory. If such file exists and remake=TRUE, the output directory is deleted and the output is recreated.

However, if the output directory outdir exists, but the status file does not, an error is reported. This is to prevent cases when an incorrect existing outdir would be delted.

cellranger_mkref to create the required reference genome directory (refdir) bamtofastq to transform mapped BAM file back into fasta files for remapping

bioDS/phyloRNA documentation built on Feb. 21, 2022, 3:28 p.m.