Jul 30, 2025

Public workspaceIGV Web Browser Tutorial

This protocol is a draft, published without a DOI.
  • Hannah Aichelman1
  • 1University of Rochester
Hannah Aichelman
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Protocol Citation: Hannah Aichelman 2025. IGV Web Browser Tutorial. protocols.io https://protocols.io/view/igv-web-browser-tutorial-g6qmbzdu7
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 30, 2025
Last Modified: July 30, 2025
Protocol Integer ID: 223725
Keywords: igv web browser tutorial protocol, igv web browser, protocol, web
Abstract
Protocol for using the IGV web browser.
Troubleshooting
Connect terminal to remote server
From your Finder, click "Go" > "Connect to server"


Select the server you want to connect to (e.g., smdnas) and login with your username and password.


Select the folder you wish to connect to on the server.


IGV Web Browser Visualizations
Go to the IGV web browser found here: https://igv.org/app/
Load in the appropriate reference genome by clicking the "Genome" menu at the top left of the webpage. Select one of the references available within IGV, or load in any custom reference that you need by loading from the "Local File..." option. Note that when you select the "Local File..." option, the remote server you connected to should appear in the side panel of your finder.


Load in the tracks that you want to visualize (e.g., bigWig, bed, narrow peak) by clicking the "Track" menu and locating the file of interest through the "Local File..." option. As above, the remote server you connected to should appear in the side panel of your finder.
You can now zoom in on specific regions or chromosomes using the search bar in the upper left-hand corner and the zoom bar in the upper right-hand corner. There are lots of helpful tutorials for IGV online, including this helpful tool: https://sandbox.bio/tutorials/igv-intro