Add custom genes to genome without whole new generate genome

[Matt K]

Hi,

I often work with transgenics and usually add the transgenes to the genome as custom chromosomes and then add entries into the gtf. This requires that I run generateGenome every time. I was wondering if there was a way to use a previously generate genome (say for human/mouse) and append on the custom transgenes? This would be both to save time and space (instead of having a bunch of custom genomes).

Thanks for your help!
-Matt

[Alexander Dobin]

Hi Matt,

yes, you can add additional FASTA and GTF at the mapping stage with

--genomeFastaFiles Extra.fasta --sjdbGTFfile Full.gtf

Extra.fasta has to include only the extra chromosomes, while Full.gtf should contain both old and extra annotations (i.e. concatenated file).

The genome will be updated on the fly and used for mapping. You can also save the new genome with --sjdbInsertSave All

Cheers

Alex

[Matt K]

That's amazing, thanks for this information.