2.2 years ago by
This prior question covers the basics for including this type of annotation in output files from this tool package. Cufflinks output files
Key point: apply the right annotation reference dataset
Detailed help that covers the full spectrum of practical usage guidance for this tool suite is in the Galaxy support wiki here https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
(Also see the "best of" help links at the top of that same wiki - many Galaxy and community resources cover RNA-seq analysis, ranging from general usage/analysis examples all the way to troubleshooting results)
Broader help/context: There are also many other posts on this forum that cover the same topic in different levels of detail. Try searching by some keywords: RNA-seq, any of these tool names, reference annotation, gene annotation, etc. Putting those terms into a google can also yield useful results (that may point back to this forum or others that cover the topic). Or try to Galaxy user search tool. Just keep in mind that the title/subject of a question or email is only about 50% related to the root issue - the content/keywords in the replies are what to focus on - which can clutter search results.
This is a very common question for users. The solution is not always the same, but give the initial advice a try then dig deeper into the others are needed. If you get completely stuck and are working on http://usegalaxy.org (or can replicate your issue there), send an email to firstname.lastname@example.org for personalized, confidential advice based on your exact data/jobs. Include a shared history link with the target datasets left undeleted, plus any other info that you think will help with context/goals.
Best, Jen, Galaxy team