# Asking for unmapped genes in RNA sequencing via Galaxy

**URL:** <https://help.galaxyproject.org/t/asking-for-unmapped-genes-in-rna-sequencing-via-galaxy/16209>\
**Category:** Uncategorized\
**Tags:** troubleshooting, mapping, transcriptomics, resources, rna\_star\
**Created:** [August 25, 2025, 7:57am UTC](https://help.galaxyproject.org/t/asking-for-unmapped-genes-in-rna-sequencing-via-galaxy/16209 "2025-08-25T07:57:22Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Atefeh\_Bahmei](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/atefeh_bahmei/32/6866_2.png) [@Atefeh\_Bahmei](https://help.galaxyproject.org/u/Atefeh_Bahmei)\
**Post date:** [August 25, 2025, 7:57am UTC](https://help.galaxyproject.org/t/asking-for-unmapped-genes-in-rna-sequencing-via-galaxy/16209/1 "2025-08-25T07:57:22Z")

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Hi. I have a RNA sequencing dataset which analyzed with Galaxy usage and type of data is paired-end. The dataset has a good quality leading to ignore the trimming level. However, after mapping with STAR tool the uniquely mapped genes were just around 6%.The mapped to loci was 3.2% and unmapped due to short reads is 90%. what should I do?

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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:** [August 25, 2025, 5:55pm UTC](https://help.galaxyproject.org/t/asking-for-unmapped-genes-in-rna-sequencing-via-galaxy/16209/2 "2025-08-25T17:55:29Z")

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Welcome @Atefeh_Bahmei

Let’s work through the problem and try to come up with some things to try. 🙂

The mapping job has four key components. Double checking each is how to troubleshoot unexpected results. Would you like to review these first, then we can follow up more?

1. **Reads**

2. **Reference genome (fasta)**

3. **Reference annotation (gff3, gtf)**

4. **Mapping tool choice and parameters**

Then, for complete protocols, the first few tutorials here are really good and each has a workflow template that can be adapted.

- [Transcriptomics / Tutorial List](https://training.galaxyproject.org/training-material/topics/transcriptomics/)

* * *

* * *

So, please review your data for these, and maybe try with HISAT2 to see if you get the same result? And you are welcome to share back your history for a closer review. → [How to get faster help with your question](https://help.galaxyproject.org/t/how-to-get-faster-help-with-your-question/11469)

Let’s start there! 🧑‍🔬