Question: Are the mkfastq
pipelines interchangeable between products?
Answer: Each mkfastq
wrapper populates the product and assay version-specific parameters for the MAKE_FASTQ_CS
pipeline invocation. For example, Long Ranger and Supernova are based on Chromium Genome assay data, and so the mkfastq
pipeline is the same for both. Meanwhile, Cell Ranger is used to process Chromium Single Cell 3' v1, 3' v2, and 5' Gene Expression and V(D)J assay data.
Thus, cellranger mkfastq
and spaceranger mkfastq
are different as the former will not be able to deal with Visium dual index sets; cellranger mkfastq
and cellranger-dna mkfastq
are different; cellranger mkfastq
and longranger
mkfastq
are not compatible; longranger mkfastq
and supernova mkfastq
are same.
Thus it is advised to use the version of mkfastq
that matches the pipeline that you are planning to run.
For more information on the parameters passed by mkfastq
to bcl2fastq
please see What bcl2fastq parameters does mkfastq use internally? If you prefer not to use mkfastq
, we recommend demultiplexing with bcl2fastq directly.