I need to analyze data from single cell RNA seq. I normally use cell ranger mkfastq to make the fastq files.
However, this time I need to make fastq files for a project that contains single indexes but was run as a dual run. The dual indexes in the run were 10 bases while the single were 8 bases. An example, of a single index used is SI-GA-F4. I found this article (https://kb.10xgenomics.com/hc/en-us/articles/115003082371-How-to-demultiplex-a-single-indexed-library-on-a-dual-indexed-flowcell-) that mentions I should be using the
--use-bases-mask= parameter. However, I am confused about what options to use.
Does that sound reasonable?
--use-bases-mask Y*,I8n*,N10, Y*