No reads show up in the workspace

[Renhao]

Hi everyone, 

I am new to IGV and using the IGV mac version. After I went to "File" -> "Load data" to load my .bam file (sorted .bam.bai is in the same directory), and zoom into under 30kb, nothing shows up in my workspace. No error popped up when loading the file, and there is a track name showed up. 

I was wondering if anyone had concurred this problem before and may help? 

Thanks in advance, 

[James Robinson]

Hi,

Usually this means there are no reads in the region you have zoomed into.    If you think there are the problem could be a mismatch between the sequence (chromosome) names your .bam file was aligned to and the sequence names in the reference genome you have selected.  If you attach a screenshot of what you see that might be helpful.   Also if possible attach the "igv.log" file, which is located in an "igv" folder in your user home directory.

Jim

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[Amy]

Hello!

I am new to IGV (just downloaded!) and experiencing the same problem. 

Things I've tried to troubleshoot but did not work:

1. Checked that the correct reference genome assembly is being used

2. Checked multiple regions, including regions of interest that I know have reads

3. Tried viewing a *.bam file that was viewable on a colleague's installation of IGV

4. Uninstalling and re-installing IGV_2.11.4 

5. Installing an archived version of IGV (2.8.13)

6. The ol' turn it off and turn it back on trick

I am using IGV_2.11.4 (with Java) on a macOS Big Sur 11.6 with an M1 chip and Rosetta installed.

Step by step of what I did:

1. Launch IGV

2. File > Load from File... 

3. Select *.bam of interest (corresponding *.bai is in same directory) --> track name corresponding to the *.bam appears

4. Navigate to gene of interest using search field at the top --> nothing appears in the loaded *.bam track (screenshot attached)

I am also attaching my IGV log file.

Thanks!

Amy

[Helga Thorvaldsdottir]

Hi Amy,

The screen shot shows you are not zoomed in far enough to see the alignments. You'll have to zoom in until the region is small enough for IGV to load the alignments.

More details: There is a limit on how much IGV can load into memory at once. The threshold for the region size where IGV will start loading the alignments is a settable preference. The default value depends on the type of data you've loaded. The overall default is 30 kb, but is higher for RNA-seq data and long read data. You can change the threshold by changing the value for "Visibility range threshold" in View > Preferences > Alignments (or RNA or Third Gen), but be aware that it will cause memory problems if you set the value too high.

Helga

[Amy]

Hi Helga,

I have also tried zooming in without success. :/

Thanks,

Amy

[Helga Thorvaldsdottir]

So what happens when you hit the threshold?  Can you send a log of just a single run of IGV where you load that file, and then zoom in beyond the threshold.

Helga

[Amy]

Hi Helga,

It works now! 

Thank you,

Amy

[Ignacio Leites]

Amy,

how do you solved it?  I have the same problem with IGV from Sophia

[Ignacio Leites]

What I see is this