mkfastq interchangeable between 10x pipelines (Cell Ranger vs. Long Ranger)?
Answer: No. The
mkfastq pipeline for Cell Ranger and Long Ranger are distinct wrappers to a common pipeline runner,
mrp, and pipeline invocation file,
MAKE_FASTQS_CS (both based on Martian).
Each wrapper populates the product and assay version specific parameters for the
MAKE_FASTQ_CS pipeline invocation. Since both Long Ranger and Supernova process Chromium Genome assay data, the
mkfastq pipeline is the same for both. On the other hand, Cell Ranger is used to process Chromium Single Cell 3' v1, 3' v2, and 5' Gene Expression and V(D)J assay data.
For more information on the parameters passed by
bcl2fastq please see What bcl2fastq parameters does mkfastq use internally?
To view the wrapper scripts for each pipeline, please see:
If you prefer not to use
mkfastq, we recommend demultiplexing with bcl2fastq directly.