Cuff Suite Not Running -- Deprecated Tool Suite

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

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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 They are no longer maintained and several include known bugs that will never be addressed.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:

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