Description of feature
When choosing the STAR-RSEM option for alignment and quantification, STAR is called through RSEM rather than directly as when choosing STAR-SALMON. This prevents, as far as I understand, modifying or adding STAR parameters because RSEM does not support extra STAR parameters. Why not modify the pipeline to call STAR directly also when quantification is performed with RSEM?
Description of feature
When choosing the STAR-RSEM option for alignment and quantification, STAR is called through RSEM rather than directly as when choosing STAR-SALMON. This prevents, as far as I understand, modifying or adding STAR parameters because RSEM does not support extra STAR parameters. Why not modify the pipeline to call STAR directly also when quantification is performed with RSEM?