Hisat and Ivar and some other tool results are viewed through IGV automatically. I am not able to view it.
Kindly guide to view results. Particularly for Ivar result, primer sequences.
Hello @abhi_g
Would you please explain a bit more about this? Maybe share an example with screenshots? I’m guessing that one of the files is not the type of data that can be visualized in IGV or there is something to review with respect to the reference genome used (and how it is annotated for the primer dataset).
Meanwhile, I’ll post a few guidelines about using IGV in Galaxy that may help to clarify common use cases.
How to view data in IGV
Through the Galaxy built-in IGV viewer
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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.
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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
- FAQ: Changing database/build (dbkey)
- How to use IGV with a custom genome database key instead of a native genome database key. → BAM index, fasta indexes, display applications, custom genome builds, IGV - #4 by jennaj
- More about how different genome assemblies can differ, using a human assembly example. → Reference genomes at public Galaxy servers: GRCh38/hg38 example
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.
This can be a bit complicated the first time through! So let us know if you have any questions or if this help to resolve the missing visualization. You are welcome to share back more about your use case and we can help! Which type of data output you have, the current metadata settings, and the URL of the server you are working at can all be factors to examine.
Let’s start there! 
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The below is being displayed. Kindly explain and guide how to view the content of the Ivar result.
I want to particularly view for the primer sequences.
Hi @abhi_g
Thanks for sharing the screenshot, very helpful!
Your BAM was originally mapped against a custom genome fasta file from the history, correct?
You have two choices:
Option 1: Configure IGV in Galaxy to use a custom genome.
This is brand new and will get easier to use with later releases.
- Open Visualize → IGV
- Choose your custom genome fasta from the history as the initial input dataset
- Expand the top section of the viewer to configure the Settings first. You will be using your custom genome fasta as the baseline for your IGV session.
- Next, toggle into the Tracks tab and add your other datasets from the history, such as your BAM from the ivar trim tool. Dragging the datasets into the visualization is what will work best right now (the datasets will not be in the pull-down menus – this is what we will be improving).
Option 2. Configure IGV in on your computer to use a custom genome.
The instructions for this method are in this topic. →
Please give this a try!
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