How to demultiplex a single indexed library on a dual indexed flow cell?

Question

[bioinfo]

Hello,

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*

Thank you

Answer 1

[GenoMax]

Use --use-bases-mask Y*,I8n*,n*,Y* (if both indexes were run as 10 bp) or use --use-bases-mask Y*,I8,n*,Y*, if first index was run 8 bp.

[bioinfo]

Thank you for the help