various BAM specific options

output files name prefix (including full or relative path). Can only be defined on the command line.

various SAM/BAM formatting options

output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). either no output or output in separate fasta/fastq files, Unmapped.out.mate1/2

string: order of multimapping alignments in the output files

int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)

which output will be directed to stdout (standard out)

path to a directory that will be used as temporary by STAR. All contents of this directory will be removed! the temp directory will default to outFileNamePrefix_STARtmp

whether to keep the temporary files after STAR runs is finished

type of SAM/BAM output