Are the references interchangeable between pipelines?

Question: Are the references interchangeable between pipelines?

Answer: In general, we recommend using the reference generated by the same pipeline. However, there is some compatibility among different pipelines: 

• cellranger mkref or spaceranger mkref create references compatible with Cell Ranger or Space Ranger, because both pipelines use STAR aligner.
• cellranger-atac mkref produces references that only work with Cell Ranger ATAC since it creates the BWA index.
• cellranger-arc mkref can generate references that contain both STAR and BWA indices. Therefore, the references generated by cellranger-arc mkref are compatible with Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC, and Space Ranger.