rsem-calculate-expression(1) on Linux
The text 331ee008dea5, as Debian 9 (Stretch) shipped it.
Flags it lists
-
--alignments -
--append-names -
--bowtie-chunkmbs -
--bowtie-e -
--bowtie-m -
--bowtie-n -
--bowtie-path -
--bowtie2 -
--bowtie2-k -
--bowtie2-mismatch-rate -
--bowtie2-path -
--bowtie2-sensitivity-level -
--calc-ci -
--calc-pme -
--ci-credibility-level -
--ci-memory -
--ci-number-of-samples-per-count-vector -
--estimate-rspd -
--fai -
--forward-prob -
--fragment-length-max -
--fragment-length-mean -
--fragment-length-min -
--fragment-length-sd -
--gibbs-burnin -
--gibbs-number-of-samples -
--gibbs-sampling-gap -
--keep-intermediate-files -
--no-bam-output -
--no-qualities -
--num-rspd-bins -
--output-genome-bam -
--paired-end -
--phred33-quals -
--phred64-quals -
--sampling-for-bam -
--seed -
--seed-length -
--single-cell-prior -
--solexa-quals -
--sort-bam-by-coordinate -
--sort-bam-by-read-name -
--sort-bam-memory-per-thread -
--star -
--star-bzipped-read-file -
--star-gzipped-read-file -
--star-output-genome-bam -
--star-path -
--strand-specific -
--tag -
--temporary-folder -
--time -
--version