Question: I have data from a 10x Genomics run which has only had 7 bases of the indexing read instead of 8. Is there a way to demultiplex within the Cell Ranger pipeline using a 7 base index?
Answer: Unfortunately, you can't use
mkfastq in this situation because it is expecting an 8 base index. However, you can use
bcl2fastq directly, and individually specify the four index oligo sequences per sample. This will require you to split each sample out into four rows (and give them individual names, e.g. suffixed with _a, _b, _c and _d) per sample. This approach will generate four sets of FASTQ files per sample.
For more information please see Using bcl2fastq directly.