Hi, I am currently trying to run RNA-SEQ on an mm39 sample. But when i use this tool with steps provided in a previous forum post linked here. Updating the mouse genome to GRCm39/mm39 on Galaxy. All that the tool produces is an ascii text file. I can not figure out what is wrong with the issue is.
Welcome, @mathew_harvey
I can reproduce what I think you are describing in this test history.
With a screenshot here showing that the downstream tool is not recognizing the index from the history.
And this one showing the file contents and creation details (i-icon).
I was working at UseGalaxy.eu. Is that also where you were working?
Let’s report the issue here. → Issues with RSEM reference index · Issue #1385 · usegalaxy-eu/infrastructure-playbook · GitHub
Thanks for reporting the problem! 
Hi, Thanks for your reply. I am working in UseGalaxy.eu and thats the same problem i am having. Is there anything else you need me to do or that would help solve the issue?
Hi @mathew_harvey Thanks for confirming the server! There isn’t anything to be done on your or my part besides reporting the issue. This tool is only hosted at the EU server (not the other UseGalaxy servers) and is a bit older. It might have larger technical issues – not sure – but the EU admins will know.
Meanwhile, I can let you know that there are alternative methods you could explore. Fully assembling the transcripts is not needed for expression analysis. Maybe consider following the analysis guides here to see if these will work for you?
This is the version you might be most interested in.
But you could also look at this one, since it includes discovery?
Then down in the advanced sections, you’ll find tutorial examples like this one. It was just updated and is another way to explore the kind of data you have. All of the reference data needed should be available for mm39.
All of these include a workflow that you could use as a template to see how the results are reported. I have run those workflows on the example data recently, and everything worked as expected but we can work through any new troubles here at this forum. Maybe also review the other end-to-end tutorials in that group to learn about other ways to calculate and visualize DE results from RNA-seq data?
Hope this helps!
Hi, Is this problem resolved?
I am trying to use RSEM-prepare reference for my data and I see that the reference prepared successfully but the Reference file size is only 17b. Is this how it is meant to be?
Is there any way I can confirm if my results are okay?
Yes, I can confirm that the indexing is still not functioning. I dug a bit deeper and the tool package is likely going to stay deprecated, despite the legacy wrappers being hosted at the EU server. I put some more comments on the ticket at the EU site. The developers will see it and either close it out or let us know if things change.
What to do for now
Try using currently supported methods instead.
The GTN tutorials linked above incorporate most of these tools, and each has some additional Help resources linked down on the tool form. If you run into problems, this forum has lots of existing help and you can ask about anything not yet clarified.
Suggested places to start would be
Not all tools have a demonstration tutorial in Galaxy, but tools work the same in Galaxy as anywhere else! That means you can use a publication’s methods, and then topics here can help with dovetailing into the downstream tools that do happen to be covered in a tutorial.
I know this isn’t the answer you wanted but I hope it helps to clarify what is going on and what the other current choices are! 
