Cuffdiff--SQLite option is buggy for all versions or just for the latest one?!

I have been trying to do some differential expression studies with my dataset’s, i have been feeding just a single replicate followed by settings as blind dispersion method ! yet the process fails each time i select generate SQLite while not selecting it and running the tools generates tabular files !

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Hello @Hart95

The tool has been deprecated for a couple of years. The creation of an SQLite database was one of the known issues that was never resolved (and won’t be).

Ticket with more details: https://github.com/galaxyproject/usegalaxy-playbook/issues/50

We strongly recommend moving to use current (and supported) differential expression tools and methods. Find tutorials that explain usage under the “Transcriptomics” topic from the GTN.

Thanks!

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Can you provide me some details for a workflow which is suitable for DE studies and can be handy with customized genomes ! Thanks for the help !

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The tutorial themselves include exact tools and associated workflows. Each tutorial starts out with an overview of the analysis concepts, then describes what parts will be specifically covered by the examples, and ends with a list of reference publications. Not every possible path is covered in detail (of course!), but combined, those resources should help you to 1) get oriented and 2) make choices that are best for your own research goals.

Please give them a review, it will be worth your time :slight_smile: Plus you can review prior Q&A at this forum. I added the tag “transcriptomics” to your post. Click on it to find similar Q&A directly, or just do a search to find even more as you progress. Many have links to FAQs and related help that can help if you run into trouble (usage, etc).

Thanks!

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