rsem-prepare-reference(1) on Linux
The text cdfd58ea85e8, as Debian 9 (Stretch) shipped it.
Flags it lists
-
--allele-to-gene-map -
--bowtie -
--bowtie-path -
--bowtie2 -
--bowtie2-path -
--gff3 -
--gff3-RNA-patterns -
--gtf -
--no-polyA-subset -
--polyA -
--polyA-length -
--star -
--star-path -
--star-sjdboverhang -
--transcript-to-gene-map -
--trusted-sources