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Question: TopHat Reference Genomes: Where has the zebrafish reference genome gone?
1
gravatar for Daniel.D.Cooper1
3.7 years ago by
Daniel.D.Cooper1 • 20
United Kingdom
Daniel.D.Cooper1 • 20 wrote:

Hello Galaxy Team,

I'm still a little new at using Galaxy, so please bear with me if this is a silly question, but I can no longer find the Zebrafish reference genome in the TopHat tool reference genome drop down menu.

The genome (danrer7/Zv9) was present back at the start of February, and it says underneath the drop-down menu that: "If your genome of interest is not listed, contact the Galaxy team" - so i hope this is the right place to do that!

Thanks for your time, I know you guys are very busy with debugging and implementing new features so i appreciate your help.

Daniel
tophat • 964 views
ADD COMMENT • link •
modified 3.7 years ago • written 3.7 years ago by Daniel.D.Cooper1 • 20

Aha! Perfect. I'll do just that then!

Thank you.

ADD REPLY • link written 3.7 years ago by Daniel.D.Cooper1 • 20
1
gravatar for Martin Čech
3.7 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

There was indeed a change. We updated Tophat to newer version (v.2) and the format of indexes changed. We are catching up on it and adding more reference genomes gradually.

In the meantime you can use custom reference genome described here: https://wiki.galaxyproject.org/Learn/CustomGenomes
ADD COMMENT • link written 3.7 years ago by Martin Čech ♦♦ 4.9k
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