RunSTARforARRIBA: RunSTARforARRIBA This function will run STAR software based...

In elmerfer/ArribaR: gene Expression quantification, Gene Fusion detection and Immuno Content Deconvolution by STAR and ARRIBA softwares

RunSTARforARRIBA This function will run STAR software based on GenomeDB

Description

RunSTARforARRIBA This function will run STAR software based on GenomeDB

Usage

RunSTARforARRIBA(sbjFile, nThreads, version = "GRCh38+GENECODE")

Arguments

sbjFile	string with the full path and name of the xxxx_1_fastq or gz sequence file. This function only support paired data
nThreads	number of CPUs threads

Details

In order to look for gene fusions with the ARRIBA software, the STAR aligner should be run with special parameters. The RunSTARforARRIBA function performe such task.

Author(s)

Elmer A. Fernández

Examples

## Not run: 
test.subject <- GetArribaRTest()
bam.subject <- RunSTAR2(test.subject)
##to display the genome and annotation version
attr(out.file,"GenomeDB")
##to display the elapsed time of the STAR run
attr(out.file,"ElapsedTime") 

## End(Not run)

elmerfer/ArribaR documentation built on Nov. 14, 2023, 1 p.m.