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:
spaceranger mkrefcreate references compatible with Cell Ranger or Space Ranger, because both pipelines use STAR aligner.
cellranger-atac mkrefproduces references that only work with Cell Ranger ATAC since it creates the BWA index.
cellranger-arc mkrefcan generate references that contain both STAR and BWA indices. Therefore, the references generated by
cellranger-arc mkrefare compatible with Cell Ranger, Cell Ranger ATAC, Cell Ranger ARC, and Space Ranger.