bamtofastq: BAM to fastq
In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

Description Usage Arguments Details See Also

Split a BAM aligned using the Cellranger software into individual .fastq files. Typically this is done to re-map and re-analyze processed data.

1	bamtofastq(bam, outdir, nthreads = 4, remake = FALSE)

`bam`	an input BAM file that was previously mapped using the Cellranger software
`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

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_count to re-map and re-analyze .fastq files.

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