rsem-prepare-reference(1) on Linux
The text 1eeb0e984123, as Debian 12 (Bookworm) shipped it.
Prepare transcript references for RSEM and optionally build BOWTIE/BOWTIE2/STAR/HISAT2(transcriptome) indices.
Flags it lists
-
--allele-to-gene-map -
--bowtie -
--bowtie-path -
--bowtie2 -
--bowtie2-path -
--gff3 -
--gff3-RNA-patterns -
--gff3-genes-as-transcripts -
--gtf -
--hisat2-hca -
--hisat2-path -
--mappability-bigwig-file -
--no-polyA-subset -
--polyA -
--polyA-length -
--prep-pRSEM -
--star -
--star-path -
--star-sjdboverhang -
--transcript-to-gene-map -
--trusted-sources