Issue viewing bam on browser (but not desktop app)

[Katie Aney]

Hello community, 

My disclaimer is that I'm a grad student who is fairly new to this type of data analysis and this is my first time running analysis using my own pipeline. 

I have a bam file where I can see signal on my IGV desktop app (2.16.1), but I am unable to see signal from the same bam (and bai) files using the browser version of IGV. My collaborator is also unable to see bam signal on their IGV desktop app. 

I have been browsing this forum for answers, so tried a few troubleshooting steps. I can make sashimi plots, but when I go to make a tdf to see read coverage in the bam file, I do not see the signal. I also do not see signal when I make bigwig files. 

I should also mention that I under-sequenced my sample and need to get more reads, so the signal is much lower than I would like. 

Here is a screenshot of my bam file in my desktop app:

And the same bam file in the browser version of IGV:

Any tips or suggestions would be very appreciated!

With gratitude,

Katie

[igv-help]

Hi Kate,

First, when you are loading the file into IGV-Web, where are you loading it from? Is it via URL or is it a local file?

It would be helpful to see if there are any error messages reported in the browser console when you try to load the file. (It varies by browser how to bring up the console. For example in Chrome: View > Developer > JavaScript Console; in Firefox: Tools > Browser Tools > Browser Console.)

The data range in the tdf track in the desktop screenshot is strange. It would be interesting to see if setting the data range on the track to 0-10 will display anything. But how did you create it from the BAM file? Did you see any error messages? Was it with igvtools from the IGV desktop application?  Make sure you are running the latest version of IGV when you do that. 

Helga