Question: How can I demultiplex a dual-indexed flowcell?
Answer: Please note that Single Cell 3' libraries, Single Cell 5' libraries, and Genome libraries are single-indexed. We do not recommend to sequence 10x Single Cell 3’ libraries with a dual-index configuration. If you run a dual-indexed flowcell but do not specify
bcl2fastq you will get this error:
[error] Dual-index flowcell detected. Please add the --ignore-dual-index option to proceed, or use an Illumina Experiment Manager-formatted sample sheet with an index2 column for the second index.
Additionally, you will need to mask the second index with
--use-bases-mask, for example:
Single Cell ATAC libraries, by contrast, are required to be dual-indexed. Please see Sequencing Requirements for Single Cell ATAC.