Question: Are the mkfastq pipelines interchangeable between products?
Answer: The short answer is that it depends. However, it is recommended to use the mkfastq that matches the pipeline and the product that you are planning to run.
Each mkfastq wrapper populates the product and assay version-specific parameters for the MAKE_FASTQ_CS pipeline invocation. For instance, the mkfastq pipeline used to process Chromium Single Cell Gene Expression data will work with both 3' and 5' products. However, older versions of cellranger mkfastq may not recognize Dual Index sets, making them incompatible with Multiome, ATAC, Visium and also probe-based assays of Visium or Flex datasets. The most up-to-date builds should be able to demultiplex them, though please note we have not tested this and this is not officially supported. Our end of life products such as supernova, longranger and cellranger-dna have mkfastq pipelines that are different from the cellranger mkfastq.
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 or bclconvert directly.
Note: Our legacy products like Linked-reads, Genome & Exome and CNV products are discontinued. We provide only limited support in these analysis pipelines.
Products: Single Cell Gene Expression, Single Cell Gene Expression Flex, Single Cell Immune Profiling, Single Cell ATAC, Single Cell Multiome ATAC + Gene Expression, Spatial Gene Expression for Fresh Frozen and FFPE
Last Updated: Aug 2024