# Generate gene to transcript map

**URL:** <https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554>\
**Category:** usegalaxy.eu support\
**Tags:** transcriptomics\
**Created:** [October 27, 2026, 6:06pm UTC](https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554 "2026-10-27T18:06:24Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![kamran.azim](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/kamran.azim/32/7589_2.png) [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\
**Post date:** [October 27, 2026, 6:06pm UTC](https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554/1 "2026-10-27T18:06:24Z")

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How does the ‘Generate gene to transcript map’ tool produces the file containing correspondence between gene ids and transcript ids based on the names of DE NOVO transcripts assembled by rnaSPAdes? The reference genome is not available.

Kamran Azim

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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 30, 2026, 4:44am UTC](https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554/2 "2026-10-30T04:44:44Z")

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Hello @kamran.azim

This tool does not interpret **rnaSPADes** assemblies.

If you do not have a reference genome, you can explore tools like **Kallisto** and **Salmon** for expression analysis using your transcriptome.

Some ideas about how to do this are discussed in the Bioconductor vignettes with more guidance at their forum here: [https://support.bioconductor.org/post/search/?query=transcriptome+expression+analysis](https://support.bioconductor.org/post/search/?query=transcriptome+expression+analysis)

Hope this helps! 🙂