# Mouse GTF reference annotation

**URL:** <https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755>\
**Category:** Uncategorized\
**Tags:** transcriptomics, reference-annotation\
**Created:** [September 27, 2022, 9:30pm UTC](https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755 "2022-09-27T21:30:52Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Brists](https://avatars.discourse-cdn.com/v4/letter/b/ecb155/32.png) [@Brists](https://help.galaxyproject.org/u/Brists)\
**Post date:** [September 27, 2022, 9:30pm UTC](https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755/1 "2022-09-27T21:30:52Z")

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Hello to the Galaxy community. Very helpful indeed. Many thanks for your effort.

I am new to sequencing and I am following the same Tutorial as above, but I am applying the protocol to mouse. Unfortunately, I ended up with the same problem, i.e., the final DEseq2 file did not contain the gene names, but instead the term N/A. I am using the file from UCSC web table, as follows:

### Dataset Peek:

| 1.Seqname | 2.Source | 3.Feature | 4.Start | 5.End | 6.Score | 7.Strand | 8.Frame | 9.Attributes |
| --- | --- | --- | --- | --- | --- | --- | --- | --- |
| chr1 | mm10\_ncbiRefSeq | stop\_codon | 134202951 | 134202953 | 0.000000 | - | . | gene\_id “NM\_001291928.1”; transcript\_id “NM\_001291928.1”; |
| chr1 | mm10\_ncbiRefSeq | CDS | 134202954 | 134203590 | 0.000000 | - | 1 | gene\_id “NM\_001291928.1”; transcript\_id “NM\_001291928.1”; |
| chr1 | mm10\_ncbiRefSeq | exon | 134199215 | 134203590 | 0.000000 | - | . | gene\_id “NM\_001291928.1”; transcript\_id “NM\_001291928.1”; |
| chr1 | mm10\_ncbiRefSeq | CDS | 134234663 | 134234733 | 0.000000 | - | 0 | gene\_id “NM\_001291928.1”; transcript\_id “NM\_001291928.1”; |

If I understood correctly I have not used the correct mouse file. Could you please help me, and point me to the correct file, and what I have done wrong, if not the wrong file?

Many thanks.

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [September 29, 2022, 12:25pm UTC](https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755/2 "2022-09-29T12:25:02Z")

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Hi @Brists,  
could you share your Galaxy history with me? My email is ![Screenshot from 2022-04-03 16-52-09](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/e/ed5122a1be2530334247fb377386743b11bae268.png).

Regards

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**Author:** ![Brists](https://avatars.discourse-cdn.com/v4/letter/b/ecb155/32.png) [@Brists](https://help.galaxyproject.org/u/Brists)\
**Post date:** [September 30, 2022, 12:24pm UTC](https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755/3 "2022-09-30T12:24:43Z")

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Hi gallardoalba,  
Thanks for your email, appreciated. Following the instructions on the help site I realised the problem was the genome reference file from UCSC table platform. I downloaded the latest mouse genome from gencode and my problems about naming of genes and unassigned ambiguity were solved. However, there are other things that I would like to ask. Therefore, I open a new topic.

Many thanks again for your effort on the help tutorials.  
Best regards,

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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:** [December 21, 2023, 1:37am UTC](https://help.galaxyproject.org/t/mouse-gtf-reference-annotation/8755/4 "2023-12-21T01:37:58Z")

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Closed on December 21, 2023, 1:37am UTC