When running Cell Ranger on O2

Shared by Victor

10x documentation is the one he uses:

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

For the custom genome:

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr

For GFP:

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#marker

Build custom genome

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

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