generateRefIndex: Build the reference genome index with STAR

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Build the reference genome index with STAR

Description

Build the reference genome index with STAR

Usage

generateRefIndex(star.path, genome.fasta, indexdir, thread = 12, ...)

Arguments

star.path	The path of the STAR.
genome.fasta	The reference genome sequence file in fasta format.
indexdir	Directory of the reference genome index.
thread	Number of CPU threads, default is 12.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Value

Directory of reference genome index

Examples

star.path='/home/dell/miniconda3/envs/scAPA/bin/STAR'
genome.fasta <- '/home/aa/genome_data/mm10/Mus_musculus.GRCm38.dna.primary_assembly.fa'
indexdir <- './mm10_index/'
## Not run: 
generateRefIndex(star.path, genome.fasta, indexdir, 24)

## End(Not run)
generateRefIndex(star.path, genome.fasta, indexdir, 24, notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.