Help with visualizing peaks

[Neha Rao]

Hello everyone, 

I am having a hard time trying to visualize the peaks of my ATAC-seq data. I tried using the .narrowpeaks and .bed files as the input files. Kindly help. 

Thank you. 

[Neha Rao]

I also tried using the .bdg files instead of the .bed files but encounter the same issue. 

[igv-help]

There doesn't appear to be any peaks at the location of your screenshot.  

[igv-help]

And from the screenshot of the whole genome view, we can see that the data is loading just fine into IGV. 

[Neha Rao]

Thank you for your response. 

I was wondering why the peaks are not visible. My coworkers who previously used this dataset for visualization did not seem to face any issues. 

[Neha Rao]

It is visible when I am viewing the whole genome but not when I zoom into a specific ROI/chromosome. 

[James Robinson]

There are no peaks at that specific locus, from your screenshot,  you can't tell that from the whole genome view.  Zoom out to you are viewing the entire chromosome, what do you see then?

[Neha Rao]

Here is what I see when I zoom out to view a particular chromosome:

On Wed, Nov 1, 2023 at 1:24 PM James Robinson <jrob...@broadinstitute.org> wrote:

There are no peaks at that specific locus, from your screenshot,  you can't tell that from the whole genome view.  Zoom out to you are viewing the entire chromosome, what do you see then?

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[igv-help]

I see a number of features there.

[Neha Rao]

How can I view the peaks in regions of interest within a specific chromosome? (I do not see any peaks when I zoom in)

[igv-help]

We can't tell from what you have shown us, whether you don't see any peaks when you zoom in because a) there are no peaks in the area you zoom into or b) there's some unknown/rare IGV issue you have run into. If you could send us a screencast that demonstrates the steps you take to zoom into an area that you know has peaks, we might be able see what's going on. It looks like you are using a Mac - the free Quicktime application provides an easy way to record an area of the screen.