How to find SAM/BAM to count matrix in Galaxy

I cant find this tool “SAM/BAM to count matrix” on my Galaxy. Has anyone experienced this?

Welcome, @obinna_1

Are you working on your own Galaxy server? Or, a public Galaxy server (actually

That sounds like a header for a section of a tutorial, not a tool name.

Do you want to clarify more? If you are following a tutorial, linking back to that is one way to do this.

Let’s start there :slight_smile:

Hi Jennaj,

I was using a workflow from a tutorial.

I am trying to count reads per gene and the tutorial showed this flow “Go to Tools → NGS Analysis → NGS: RNA Analysis → SAM/BAM to count matrix.”

Hi @obinna_1 Would you please share a link to that tutorial? Sorry to be picky but I’m not able to find it :slight_smile:

Hi @jennaj,
Please see attached the link.

Hi @obinna_1

Thanks for sharing that link.

It looks like that tutorial was created for the server, but some version of that Galaxy I haven’t seen before. Odd. I didn’t explore too much.

You could probably still follow most of it many servers, but maybe not if you are brand new to Galaxy. Some parts miss functionality, and this tool is not available and it does two things at once. Specifically, the part about not being able to use HTseq-count with multiple BAMs seem to not synch up with the regular usage (even much older versions of public Galaxy servers).

What to do:

  1. Consider using HTseq-count instead, and merge the counts into a matrix after. If you use collections, group tags could be used instead.
  2. Consider following an updated version of that protocol as hosted at the GTN. This will work fine at any of the UseGalaxy servers, and many others too.
  3. I remember the tool now … vaguely, but can’t remember where I used it or exactly how long ago that was, but at least 5 years. If someone else knows, please comment!

Learn at GTN →

Hope that helps!

Thank you very much @jennaj for taking out time to put me through and pointing me in the right direction. I will review the attached links and try the methods therein.

I will revert back with an update when I am done.

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