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! 