Basic Comparative Transcriptomic Analysis Workflow

I am having difficulties with comparative transcriptomic analysis between two types of Myxococcus species. Maybe they are too different to compare. It is the M. xanthus and M. stipitatus species. Could someone please post a simple workflow that they would use on galaxy to process and visualize this comparison.

I have been using the fna and gtf files, is there another file that I must include?

Hi @Ian_Hochwender

If you are working from the tool panel view (searching tools, or found one already that you think is interesting), scroll down into the Help section for usage help. That can include notes from the wrapper author, examples, usage tips, links out to the original authors resources (tutorials, publications), and link to GTN tutorials that tool is included in (if any).

Tools in the Multiple Alignment tool groups are probably what you are looking for specifically. Different public servers can host different tools – so if you have some publication that you are following, and don’t find the tool at one, you can check the others for that exact tool or similar tools. You’ll only find open source tools at the public servers.

Available GTN tutorials are here, and most include a workflow template: Galaxy Training!. The categories that are probably most relevant to you are Assembly, Variant Analysis, and Evolution.

Galaxy publications are listed here: Galaxy Publication Library - Galaxy Community Hub. The last “using Galaxy” publication includes a section covering cross-species MAF alignments. Not quite the same as comparing transcriptomes, but might still be useful.

Also, keep in mind that it is super easy to create a workflow from existing work. Extract from history → tune → annotate → publish. The GTN site above has full instructions.

More places to find existing workflows:

Hope that helps!