# Can the latest gtf file be used as the annotation file with the old reference genome available in galaxy?

**URL:** <https://help.galaxyproject.org/t/can-the-latest-gtf-file-be-used-as-the-annotation-file-with-the-old-reference-genome-available-in-galaxy/11737>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, transcriptomics\
**Created:** [February 17, 2024, 10:46am UTC](https://help.galaxyproject.org/t/can-the-latest-gtf-file-be-used-as-the-annotation-file-with-the-old-reference-genome-available-in-galaxy/11737 "2024-02-17T10:46:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Sanjukta\_Ghosh](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sanjukta_ghosh/32/4454_2.png) [@Sanjukta\_Ghosh](https://help.galaxyproject.org/u/Sanjukta_Ghosh)\
**Post date:** [February 17, 2024, 10:46am UTC](https://help.galaxyproject.org/t/can-the-latest-gtf-file-be-used-as-the-annotation-file-with-the-old-reference-genome-available-in-galaxy/11737/1 "2024-02-17T10:46:29Z")

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Hi, I am performing reference based RNA-Seq.  
In that I am using mm10 (MusMusculus10) as my reference genome and want to use [GRCm39.111.gtf.gz](https://ftp.ensembl.org/pub/release-111/gtf/mus_musculus/) as the annotation file. Will it be compatible?

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**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [February 19, 2024, 6:53am UTC](https://help.galaxyproject.org/t/can-the-latest-gtf-file-be-used-as-the-annotation-file-with-the-old-reference-genome-available-in-galaxy/11737/2 "2024-02-19T06:53:20Z")

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Hi @Sanjukta_Ghosh  
generally, the answer is No. There are some exceptions when genome coordinates stay the same, but these exceptions are (extremely) rare. Data must be from the same version of a genome assembly.  
Either use annotation for mm10, or import GRCm39 genome assembly (fasta file) into your history, and during setup of alignment job (with HiSAT2 or similar tool) change Source of reference genome from Built-in to In History. The BAM file will be compatible with GRCm39 annotation.  
Kind regards,  
Igor