"Introduction to Genomics and Galaxy" GENCODE V41 unavailable

Hi, when following the " Introduction to Genomics and Galaxy" tutorial, it states we should use GENCODE V41 track, however this is not an available option.
Is there an alternative? TYIA

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Hi @Mehgan

Yes, that discussion is complicated. I had to re-read it a few times to remember the issue! I’ll try to explain in a slightly different way here…

  1. All GENCODE and GENCODE are two different tracks that contain different data but are named in a similar way and are created by the same data provider.

  2. UCSC only hosts the “most current” version of the GENCODE track (even though I see two today, captured in my screenshot)

  3. The screenshot in the tutorial has GENCODE v32 selected but that version is not available anymore.

Then the answer becomes → Choose the most current available version of a tracked named like GENCODE vNN. Today, that happens to be GENCODE v44.

That could probably be added to the tutorial. I’ll make the edit suggestion for later on.


Feel free to ask more new questions here if something like this comes up again :slight_smile: The tutorials are trying to simplify somewhat complex concepts, all while the data underneath is changing. We could just supply the reference file, and some tutorials will do that, but the data would become stale over time, and you wouldn’t learn how to get similar files yourself when doing actual analysis on new data.

You’ll learn more about what to watch out for as your data scientist skills are developed. Everyone doing analysis has to learn this stuff, and in some ways it never stops changing! But you’ll train your eye with experience.

Amazing @jennaj! Thank you