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Question: No "local" option to view BAM files with IGV
0
gravatar for Chris
3.6 years ago by
Chris • 0
United Kingdom
Chris • 0 wrote:

Hi

I have BAM files loaded onto the main Galaxy server usegalaxy.org) and I want to visualize them in my local copy of IGV. However, there is currently no "web current" or "local" hyperlinks next to the IGV option, there is only a link with the name of the genome that the BAM is aligned to i.e "Zebrafish (Zv9/danRer7)". I have not had this problem in the past, but the BAM files have come from a different source this time. Does anyone know if this is a Galaxy error or a problem with my BAM files?

Thanks

Chris

 
igv galaxy bam • 1.1k views
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modified 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.6 years ago by Chris • 0
1
gravatar for Daniel Blankenberg
3.6 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Chris,

We have restored the 'local' links for IGV display. The 'web current' link has been replaced with the Genome/Build Name as declared by IGV's available genome list, so the 'Zebrafish (Zv9/danRer7)' link is equivalent to the old 'web current'.

Please let us know if you encounter additional issues.

 

Thanks for using Galaxy,

Dan
ADD COMMENT • link written 3.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Thanks Dan, that is great!

Chris

ADD REPLY • link written 3.6 years ago by Chris • 0
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