# rMATS in Docker Galaxy troubleshooting

**URL:** <https://help.galaxyproject.org/t/rmats-in-docker-galaxy-troubleshooting/16413>\
**Category:** Uncategorized\
**Tags:** troubleshooting, rmats\
**Created:** [October 22, 2025, 4:13pm UTC](https://help.galaxyproject.org/t/rmats-in-docker-galaxy-troubleshooting/16413 "2025-10-22T16:13:01Z")\
**Posts on this page:** 1\
**Showing post:** 4

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 23, 2025, 9:34pm UTC](https://help.galaxyproject.org/t/rmats-in-docker-galaxy-troubleshooting/16413/4 "2025-10-23T21:34:40Z")

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Thanks for sharing the screenshots @Dongqi_Xie !!

On the tool form, the select field will list all _potential_ input datasets. These will always be datasets present in the active history and with an assigned datatype that matches one of the “accepted datatypes” for that input field.

Then, from the listing, you can select the input datasets to actually use by clicking on them from the listing pull-down menu.

And to review the inputs and parameters that were applied for a job, reviewing the job’s Details view will have a table of those settings. You have this in one of your screenshots. This is a screenshot of your screenshot of the relevant section:

 ![Screenshot 2025-10-23 at 2.10.11 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/347e2c66a5057aff96641731c84c9034698e1f51.png)

- You are also using a `gtf` dataset that was sourced from **Gencode** that is based on the **Homo Sapiens GRCh38 hg38** assembly. This is your **reference annotation**.

- It seems you have selected two replicates from two different samples for a total of four `bam` dataset files.

Other than that, different parameters can impact the results of course! The original manual from the tools and potentially online discussion at a scientific forum like [Biostars.org](http://Biostars.org) are the resources to review to learn about fine tuning for specific outcomes. The tool will work in Galaxy about the same as anywhere else. Or, _should_. If you notice some bug with the tool wrapper, you can report this to the developer at their Github repository.

**Xref**

- [GitHub - Xinglab/rmats-turbo](https://github.com/Xinglab/rmats-turbo?tab=readme-ov-file#all-arguments)
- Example discussion at the author Github about reference data, parameters, and how the tool is processing the data. If I am understanding correctly, they seem to think Gencode is a good annotation choice! → [rMATS Reference Files – Clarification · Issue #521 · Xinglab/rmats-turbo · GitHub](https://github.com/Xinglab/rmats-turbo/issues/521)

* * *

So – I think the tool is working as expected! Please let us know if this helps or not. 🙂

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