# 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:** 3\
**Page:** 1

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**Author:** ![poojashukla](https://avatars.discourse-cdn.com/v4/letter/p/94ad74/32.png) [@poojashukla](https://help.galaxyproject.org/u/poojashukla)\
**Post date:** [July 25, 2026, 5:02am UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210/1 "2026-07-25T05:02:44Z")

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i want to know when i am doing stringtie and uploading GTF file of zebrafish genome its giving error or not matching notations with hisat2 in built genomic sequence, help me find zebrfish gemome GTF file that matches to european galaxy in built zebrafish genome

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**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\
**Post date:** [July 27, 2026, 4:10pm UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210/2 "2026-07-27T16:10:13Z")

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currently being answered in Lobby channel on Matrix …

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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! 🙂