How to demultiplex a single indexed library on a dual indexed flow cell?
1
0
Entering edit mode
8 weeks ago
bioinfo ▴ 10

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

Cell Single • 390 views
ADD COMMENT
0
Entering edit mode
8 weeks ago
GenoMax 111k

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.

ADD COMMENT
0
Entering edit mode

Thank you for the help

ADD REPLY

Login before adding your answer.

Traffic: 1780 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6