cellranger_mkref: Generate Cellranger Transcriptome Reference Genome

In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description

Run cellranger mkref and generate the Cellranger Transcriptome Reference Genome.

Usage

cellranger_mkref(reference, annotation, outdir, nthreads = 4, remake = FALSE)

Arguments

reference	a reference genome fasta file (e.g., .fna)
annotation	a GTF (.gtf) annotation file associated with the reference genome
outdir	a non-existing output directory, see details
nthreads	optional a number of threads to run on
remake	optional remake the output if it already exists

Details

The reference which must include associated index file (fai) in the same directory.

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.

See Also

cellranger_count to use this reference directory to perform an expression analysis bamtofastq to transform mapped BAM file back into fasta files for remapping

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