Cuff Suite Not Running -- Deprecated Tool Suite

[rpotens007]

Cufflinks, Cuffcompare, and Cuffnorm stopped running. I tried resume paused jobs but still paused.

[jennaj]

Hi @rpotens007

All of these tools are deprecated and should be avoided. They are no longer maintained and several include known bugs that will never be addressed.

Even if they work (do not fail or stall out), unexpected scientific results can occur that are not always obvious to detect.

Try the updated methods in the “Transcriptomics” GTN tutorials instead:

@jennaj

Galaxy Training Network Tutorials: Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

Troubleshooting tips that cover the updated tools/methods should you run into problems:

• Extended Help for Differential Expression Analysis Tools