When running Cell Ranger on O2

Shared by Victor

10x documentation is the one he uses:

For the custom genome:

For GFP:

High level steps (based on the 10x tutorial):

Download the gtf and fasta files for the species of interest;
Filter gtf with cellranger mkgtf command;
Create the fasta file for the additional gene (for example, GFP);
Create the corresponding gtf file for the additional gene;
Append fasta file of the additional gene to the end of the fasta file for the genome;
Append gtf file of the additional gene to the end of the gtf file for the genome;
Make custom genome with cellranger mkref command;