# Fail to load GFF3 into IGV

**URL:** <https://help.galaxyproject.org/t/fail-to-load-gff3-into-igv/13450>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, igv\
**Created:** [September 14, 2024, 10:33pm UTC](https://help.galaxyproject.org/t/fail-to-load-gff3-into-igv/13450 "2024-09-14T22:33:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Roman4O](https://avatars.discourse-cdn.com/v4/letter/r/858c86/32.png) [@Roman4O](https://help.galaxyproject.org/u/Roman4O)\
**Post date:** [September 14, 2024, 10:33pm UTC](https://help.galaxyproject.org/t/fail-to-load-gff3-into-igv/13450/1 "2024-09-14T22:33:33Z")

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Hi,  
I’m trying to add a new genome to IGV using this protocol: [FAQ: Add genome and annotations to IGV from Galaxy / Visualisation](https://training.galaxyproject.org/training-material/topics/visualisation/faqs/visualizations_igv_add_genome.html). 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?

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [September 16, 2024, 7:31pm UTC](https://help.galaxyproject.org/t/fail-to-load-gff3-into-igv/13450/2 "2024-09-16T19:31:29Z")

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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?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)

Then, your GFF3 needs to be based on that exact same genome.

More instructions are in this topic

> [@Is there a way to use the display in IGV tool so I don't have to download the genome separately?](https://help.galaxyproject.org/t/is-there-a-way-to-use-the-display-in-igv-tool-so-i-dont-have-to-download-the-genome-separately/10710/2):
>
> **How to link data between Galaxy and IGV**
> 
> **Single file display** based on coordinates _without_ base-level details
> 
> 1. Use the link to IGV under a dataset’s visualization display function
> 2. Wait for the one-off indexing to complete, and you’ll be automatically redirected
> 
> **Single or Multiple file display** based on coordinates _with_ base-level details
> 
> 1. Reference Genome is indexed in IGV (native or custom)
> 2. Reference Genome is indexed in Galaxy (native or custom)
> 3. Reference Genome is exactly the same assembly/build and given same database (dbkey) in both
> 4. Dataset(s) assigned that database (dbkey)
> 5. Use the link to IGV under a dataset’s visualization display function

* * *

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](https://help.galaxyproject.org/docs?topic=11469)

Let’s start there, thanks! 🙂