techblog2022-05-20

Changing STAR Parameters in CellRanger

Cell Ranger is a tool that anyone familiar with single cell RNA-seq will know. I had never used it before, but decided to give it a try. However, it internally uses STAR for mapping, and there is a problem (that nobody else seems to mind) where you cannot pass STAR parameters as arguments. The official answer is to build it yourself, though they take no responsibility for it.