Create a standard directory for bears
Arguments
- rootdir
Root directory where all subdirectories will be created. If not specified, a directory named "results_YYYY-MM-DD" will be created, where Y, M and D represent year, month and day, respectively.
Value
A list of paths with following elements:
- fastqdir
Path to directory where FASTQ files are.
- qcdir
Path to directory where QC and summary statistics will be stored.
- filtdir
Path to directory where filtered FASTQ files are.
- mappingdir
Path to directory where STAR-derived BAM files are.
- salmonindex
Path to directory where salmon transcriptome index is.
- salmondir
Path to directory where salmon output files are.
- kallistoindex
Path to directory where kallisto transcriptome index is.
- kallistodir
Path to directory where kallisto output files are.
- fcountsdir
Path to directory where featureCounts output files are.
- stringtiedir
Path to directory where StringTie output files are.
Examples
rootdir <- tempdir()
dirs <- create_dir_structure(rootdir)