Hi,
I’m trying to add a new genome to IGV using this protocol: FAQ: Add genome and annotations to IGV from Galaxy / Visualisation. However, it’s taking too long to load the GFF3 file (several hours). It’s still loading. I’ve tried 2.14 and 2.18 versions of IGV with no result. What could be the underlying cause of this issue?
Welcome, @Roman4O
Has this completed yet?
You reference genome fasta should be formatted in a very simple way. We have a guide here → FAQ: How to use Custom Reference Genomes?
Then, your GFF3 needs to be based on that exact same genome.
More instructions are in this topic
Why this is taking a while could be a content issue – but not just with the format, instead – is there anything special about this data? A high number of chromosomes? Really long chromosomes (some plants fall into this category)? Are you able to load the same genome directly into IGV? (often a better choice, the reasons are in that topic above in the discussion)
For more help here, you can share your history with the fasta and GFF3 data, and we can help to troubleshoot content problems. How to do this is in the banner at this forum, or please see here directly → How to get faster help with your question
Let’s start there, thanks! 