Filter with SortMeRNA option for generating statistics file missing

Tool Filter with SortMeRNA states that “Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.”. That option is also mentioned in, for instance, Galaxy Training “Metatranscriptomics analysis using microbiome RNA-seq data” ("Generate statistics file”: Yes).

However, I do not find that option in the tool’s options section. I am pretty sure it used to be there, though.

Am I missing something or is that option indeed missing for some reason?


Hi @jmuser

That tutorial uses an earlier version of the tool wrapper (and underlying tool).

Any of the versions named like 2.1b.N have the legacy statistics option are you looking for. How to → FAQ: Changing the tool version

Please give that a try and let us know if helps you to solve the problem. Thanks!

Hi @jennaj
Thanks a lot! Galaxy Version 2.1b.6 and earlier indeed have the Generate Statistics option that I was looking for.
Is there a particular reason why it was omitted from the latest v4.3.6+galaxy0? The statistics option appears quite useful.

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Hi @jmuser I think the underlying tool updated, and the additional statistics reports were no longer available. I can’t remember the full details but it has come up before. I checked and that discussion wasn’t at the forum. Probably in a long lost chat, and that would just be the Galaxy part anyway, not the real reason.

If you really want to know, it might be somewhere else online. I would start at the primary development site for the tool. Find the link at the bottom of the tool form, or just internet search.

We miss it too. Creates a bit of confusion when supporting the tool as hosted in Galaxy…