RNA-seq analysis (minimap2, featurecounts, deseq2) result differences

1

Hello, I’m doing an RNA-seq analysis (minimap2, featurecounts, deseq2) using the pipeline of a colleague. She got different results, while the data and settings are the same.

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Hi @CarinaS

with “pipeline” you mean a Galaxy workflow?

3

Hi wm75, yes, that’s what I mean. I’m wondering if there have been changes in the tools since September, which is when my colleague ran her analysis.

4

Hmm, if it’s a Galaxy workflow and neither you nor your colleague did update it since her analysis, then that should not be an issue.
You haven’t specified yet which server this is happening on. Is it the same one for both of you?
Also, any chance that you can share the workflow (not the data)?

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I’m pretty new to Galaxy, where can I find which server I’m on?
And I also don’t know how I can share a workflow, I have made screenshots of the settings we’ve used, I can share those if that helps.

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Well, the server address is in your browser navigation bar (usegalaxy.org, usegalaxy.eu, etc.)

You can share a workflow from the “My workflows” list, where each workflow has a share icon. “Make workflow accessible”, then sharing the url that gives you here, would be fine.

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Ah okay, the server is usegalaxy.eu. And concerning the workflow, we did not work with the workflow option. She made a text file explaining the pipeline and this is what I used. So all the tools are in my history separately.

8

I see. Then your only option really is to carefully inspect every steps inputs and outputs and nail down where differences occur. You might have made a mistake at any step or, as you were suggesting above, one of the tools you used may have been updated in the meantime. Galaxy not only records all input params, but also exact tool versions used.

It’s just a lot of work to compare everything and a workflow instead of written-down instructions would have saved you a lot of time.

Consider working through one of the introductory Galaxy tutorials like Hands-on: Galaxy 101 / Introduction to Galaxy Analyses to learn about the features (like workflows) you’ve missed out on so far.

Best,
Wolfgang

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Dear Wolfgang,

Thank so much for helping and the tutorial suggestion. I agree that a workflow would have been much better and saved us time. I am making one now.

Have a nice day!
Carina

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