14 months ago by
Was this the reference tutorial video? https://www.coursera.org/learn/galaxy-project/lecture/VxxpN/rna-seq-analysis-mapping
The tools used in this tutorial are available at the Main Public Galaxy server http://usegalaxy.org. Which one is missing? Tophat for Illumina has been replaced with Tophat2 (named simply Tophat). If another tool is missing, it may be in other tool groups. Search by the tool name (top of the left tool panel) to locate. The Coursera tutorial is great to learn with plus there are other current RNA-seq tutorials for Galaxy that can be found here: https://galaxyproject.org/learn/
If working on a local or cloud Galaxy, any missing tools may need to be installed, by you or the administrator of the server.
If working at another Galaxy server (public or at your institution), you could ask the administrators of that server if the tools needed could be added. Note that many public servers are customized for a specific analysis workflow and may not include RNA-seq tools (and in many cases will not be modified).
For many use cases, Tophat has been replaced by HISAT when performing RNA-seq analysis. Please see the latest Tophat and HISAT release notes for details and links to related publications and user manuals. HISAT2 is available at http://usegalaxy.org and is in the Galaxy Toolshed where it can be installed in a local/cloud/another Galaxy server. The best practice workflow may have been updated since any tutorial you find was published, yet the original tools are still available (on the server you are using, or in the Tool Shed) if you wish to use the original methods.
We hope this helps. Please let us know if you need more information. Thanks! Jen, Galaxy team