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Question: IGV option doesn't appear after uploading the BAM file
1
gravatar for cindy.castelao
3.7 years ago by
cindy.castelao • 10
Portugal
cindy.castelao • 10 wrote:

Hello,

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,

Cindy
igv bam • 1.2k views
ADD COMMENT • link •
modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by cindy.castelao • 10
1
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.

 

Thanks,

 

Dan
ADD COMMENT • link 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?

Thanks

Chris

ADD REPLY • link written 3.7 years ago by Chris • 0

Same Issue!

ADD REPLY • link written 3.6 years ago by madkisson • 30

Hello, Changes and corrections take some time to propagate to the Galaxy release branches and then to the public Main Galaxy server at http://usegalaxy.org (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):
http://getgalaxy.org General
http://wiki.galaxyproject.org/DevNewsBriefs Specific per-release, including changes made between releases but that are in the "stable" branch.

Dan may add more!

Thanks, Jen, Galaxy team

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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