Question: IGV option doesn't appear after uploading the BAM file
gravatar for cindy.castelao
3.7 years ago by
cindy.castelao10 wrote:


After uploading the BAM files, and choosing my genome database it used to appear the IGV option to locally open my file. However, since yesterday, this option doesn't appear.

I was hoping for your help , as I need to run my BAM files in the IGV software as quickly as possible.

Thank you very much,


igv bam • 1.2k views
ADD COMMENTlink modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by cindy.castelao10
gravatar for Daniel Blankenberg
3.7 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Cindy,

Thanks for reporting this issue, it should be resolved now. Please let us know if you encounter additional difficulties.





ADD COMMENTlink written 3.7 years ago by Daniel Blankenberg ♦♦ 1.7k

Hi Dan,

I am currently having the same problem i.e. the IGV "local" link does not appear next to my bam files. Has the problem come back again, or is this a separate issue unique to me?



ADD REPLYlink written 3.7 years ago by Chris0

Same Issue!

ADD REPLYlink written 3.6 years ago by madkisson30

Hello, Changes and corrections take some time to propagate to the Galaxy release branches and then to the public Main Galaxy server at (if that is where you are working). Also, the "database" assignment must match the genome loaded into IGV. And if by chance you are using a local, that type of server would need to be updated against the latest code branch for the fix to be in place on your server. 

Hello for upgrading and staying current for locals (if using one): General Specific per-release, including changes made between releases but that are in the "stable" branch.

Dan may add more!

Thanks, Jen, Galaxy team

ADD REPLYlink written 3.6 years ago by Jennifer Hillman Jackson25k
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