Question: TopHat Reference Genomes: Where has the zebrafish reference genome gone?
gravatar for Daniel.D.Cooper1
3.7 years ago by
United Kingdom
Daniel.D.Cooper120 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.


tophat • 964 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Daniel.D.Cooper120

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

Thank you.

ADD REPLYlink written 3.7 years ago by Daniel.D.Cooper120
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:

ADD COMMENTlink written 3.7 years ago by Martin Čech ♦♦ 4.9k
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