Question: I sequenced my dual indexed library as an 8bp single index. Will reading only the first 8bp of the 10bp index read be sufficient for demultiplexing?
Answer: Yes, you can de-multiplex even if only the first 8bp of the i7 index are sequenced. The dual index plates are designed such that the index sequence would be unique even if only the first 8bp of i7 were sequenced. However, since you will be demultiplexing using only a single index, you will lose the benefit of dual indexing in removing potential index hopped reads.
You will need to enter the first 8 bases of the sample index in the sample sheet to run mkfastq/bcl2fastq.
Please note that the information above does not apply to ATAC sequencing. For single assay ATAC or multiome ATAC sequencing, it is mandatory to have 8 bp on i7 reads for demultiplexing, and 16bp on i5 reads for cellular barcodes.
Products: Single Cell Gene Expression, Single Cell Immune Profiling