jennaj
March 5, 2026, 8:33pm
2
Hello @abhi_g
If you bam is not displaying yet, this means you need to configure IGV to be based on your reference genome. This can be a fasta file from the history, or a native index on the server.
Which reference genome are you currently using for mapping? Do you want to share some screenshots?
More help was in a recent topic but we can help you to navigate the instructions if we learn more about what you have now.
Let’s start here!
How to view data in IGV
Use the eye icon in the upper right corner of a dataset. Some data will automatically display under the Preview tab. For others, you can first click into the Visualize tab, then either 1) launch a new IGV application session 2) or join one already started up 3) or connect to your local IGV session. More about this below with a screenshot.
The dataset needs to represent data that is based on a reference genome assembly’s coordinates and that database key needs to be assigned. This is how the data is associated with a specific fasta index for that genome assembly.
How to troubleshoot
Review the datatype format of the dataset. Is this coordinate based data?
Review the database assignment. Is the data linked to a reference genome assembly? Has the dataset been annotated with this assignment?
If the data was generated in Galaxy using a native database key, then the key should already be assigned.
In some cases, you may be able to make a direct direct database assignment. This could include data processed somewhere else and Uploaded to Galaxy.
This works in Galaxy the same as it does when using IGV independently. Data is all based on the same assembly, and the coordinates are used to map the data to the genome’s base pairs in a fasta file. Try to avoid viewing data from different assemblies together. Why? A different assembly will use a different coordinate system. Attempting to view mixed data may result in an error or it may only have odd results in the display.
Resources
Screenshot
This is an example for a BAM database with the native database key dm6 assigned. This dataset can be individually viewed under the Preview tab. Then, under the Visualize tab, the dataset could be viewed in a local IGV session or added to a Galaxy IGV session that includes multiple datasets all together.
If I had a custom genome key instead, then I would choose to use the local IGV session option (option 2. display with IGV – using the “local” link) – after setting up my custom genome build in Galaxy and IGV (both!). The custom build key is what informs both applications that the data is based on the same fasta index.
