Trouble Seeing Gene Annotations After Loading Reference Genome

[Lilian Souza]

Hi everyone,

I'm using IGV to analyze Saccharomyces cerevisiae whole-genome data. I’ve loaded my reference genome (ref.genome.fa) and can see my VCF and BAM tracks fine, but I’m not seeing any gene annotations.

I’m wondering:

• Do I need to load a GFF or GTF file manually for annotations to appear?

• Do the chromosome names in the FASTA and annotation file need to match exactly?

• Is there a specific file or step required to display gene features?

Any help or suggestions would be appreciated!

Best,
Lilian

[igv-help]

If you load your reference genome via a FASTA file, then you will also need to load your own gene annotations e.g. GFF or GTF file.

I don't know if you have a special version of the Saccharomyces cerevisiae  genome, but if you load the one from the Genomes > Load Hosted Genome in IGV (sacCer3) it will come with a default gene track. Also - assuming you are running IGV 2.19.x - there are a number of Saccharomyces cerevisiae  assemblies available through Genomes > Load Genome from UCSC GenArk and each one has a selection of annotation tracks you can select.

Helga