RunSTAR: RunSTAR

In elmerfer/Aligners:

RunSTAR

Description

RunSTAR

Usage

RunSTAR(sbjFile, species, version, twoPass = c("None", "Basic"), nThreads)

Arguments

sbjFile	string full path to the R1.fastq or or gz file
species	the species you whant to use, it should be stored in your database pls see ShowSpecies
version	the code indicating the genome+annotation pair
twoPass	"None" or "Basic". If set to "Basic", Annotated junctions will be included in both the 1st and 2nd passes. To run STAR 2-pass mapping for each sample separately. STAR will perform the 1st pass mapping, then it will automatically extract junctions, insert them into the genome index, and, finally, re-map all reads in the 2nd mapping pass. This option can be used with annotations, which can be included either at the run-time or at the genome generation step.
nThreads	integer, number of CPUs to be used

Value

the file name of the resulted bam file with an attribute "assemblyVersion" that shows the reference-annotation verision see GetGenomesInDB

elmerfer/Aligners documentation built on May 27, 2023, 5:05 a.m.