<p>It wasn't the correct file.
I downloaded the file again from UCSC, compared it with the file that I was using, and they were different. This new file contained both information from coding and non-coding transcripts.</p>
<p>To all the kind people that took interest in my problem, I am sorry.</p>
<p>Edited 30/12/2020:
To add a bit of clarity; the link in the question is the correct link from which to download the correct file. The file with which I was working from the beginning was the wrong one, but I don't really know where I got it from the first time.</p>

CC BY-SA 4.0
2019-04-05T13:06:17.637Z
2020-12-30T12:29:39.760Z
2020-12-30T12:29:39.760Z
jorvaor
<p>I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species.</p>

<p>My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome. I have seen that the Human one (hg39) contains both coding and non-coding transcripts. But the Mouse (mm10) RefGene.txt only contains coding transcripts.</p>

<p>Why is that?</p>

<p>Source of the file: <a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz" rel="nofollow noreferrer">http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz</a></p>

CC BY-SA 4.0
2019-04-02T11:31:27.480Z
Is there a reason you're using refseq rather than the more complete annotations from Ensembl/Gencode?
Devon Ryan
CC BY-SA 4.0
2019-04-02T12:02:08.223Z
Yes, it is an exercise in a course. I am to use bash shell and gawk to extract some information from several refGene.txt files.    The question about the absence of non-coding transcripts in mouse is not part of the exercise, but have puzzled me. I have been looking for info about it, but I haven't a clear explanation.
jorvaor
<sequence-annotation>
Why doesn't the mouse GRCm38/mm10 refGene genome annotation file contain non-coding transcripts?
# Why doesn't the mouse GRCm38/mm10 refGene genome annotation file contain non-coding transcripts?

(Asked by: username_0 on 2019-04-02)

I am new to Bioinformatics and I am exploring the refGene.txt files from the UCSC genome annotation database for several species.

My question concerns the Dec. 2011 (GRCm38/mm10) assembly of the mouse genome. I have seen that the Human one (hg39) contains both coding and non-coding transcripts. But the Mouse (mm10) RefGene.txt only contains coding transcripts.

Why is that?

Source of the file: <http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz>

**Tags:** sequence-annotation
> **Comments:**
> **username_1**: Is there a reason you're using refseq rather than the more complete annotations from Ensembl/Gencode?  
> **username_0**: Yes, it is an exercise in a course. I am to use bash shell and gawk to extract some information from several refGene.txt files.    The question about the absence of non-coding transcripts in mouse is not part of the exercise, but have puzzled me. I have been looking for info about it, but I haven't a clear explanation.  

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## 1 answers

### Answer by username_0 on 2019-04-05. Score: 1

It wasn't the correct file.
I downloaded the file again from UCSC, compared it with the file that I was using, and they were different. This new file contained both information from coding and non-coding transcripts.

To all the kind people that took interest in my problem, I am sorry.

Edited 30/12/2020:
To add a bit of clarity; the link in the question is the correct link from which to download the correct file. The file with which I was working from the beginning was the wrong one, but I don't really know where I got it from the first time.


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