# Stringtie help related to GTF file for zebrafish genome

**URL:** <https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210>\
**Category:** Uncategorized\
**Tags:** transcriptomics, stringtie\
**Created:** [July 25, 2026, 5:02am UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210 "2026-07-25T05:02:44Z")\
**Posts on this page:** 1\
**Showing post:** 3

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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:** [July 28, 2026, 8:30pm UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210/3 "2026-07-28T20:30:55Z")

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XRef [You're invited to talk on Matrix](https://matrix.to/#/!IEcbSOGXlqPpSmwmPp:gitter.im/$YZX9kZ-o311QISo98dp7yKDr29ETVgu02z0eCiLUJYE?via=gitter.im&via=matrix.org&via=sys.reslate.net)

For your followup question @poojashukla about the predicted transcript identifiers (MSTRG), what to do next depends on what you have already done!

If you haven’t run a merge step yet (predicted along with known to “merge”), then you can do that. If the predicted transcripts overlap with a known transcript, the annotation will be merged and the known label applied.

Some features might not merge into a known gene bound. Those are your **predicted novel** features.

You can generate your final counts to use for DE against the merged version of the annotation (novel + known) or you can just use the known. Maybe do both and compare?

Similar topics have this same advice. [Search results for 'stringtie mstrg' - Galaxy Community Help](https://help.galaxyproject.org/search?q=stringtie%20mstrg)

> [@MSTRG to Gene Name Conversion](https://help.galaxyproject.org/t/mstrg-to-gene-name-conversion/3013/6):
>
> Do you mean that some transcript/genes have known annotation labels and some don’t? If so – that would be due to novels in your data. If there is no known annotation for certain features, those won’t have a known attribute like gene or transcript name.

This tutorial goes through the process. → [Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html)

Hope this helps! 🙂

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