<p>It would be helpful to know</p>
<ol>
<li>what you mean by &quot;name&quot;- like a non-systematic gene symbol (&quot;P53&quot;) or a systematic identifier (&quot;NP_000537.1&quot;)?</li>
<li>exactly which strains you are working with. Wormbase does not seem to have very many diverse genome assemblies for C. elegans readily available. (Note that I am not a worm/wormbase person, maybe I'm missing something.)</li>
</ol>
<p>But gene orthology for the main genomes is given directly in <a href="https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species/caenorhabditis_elegans/PRJNA13758/caenorhabditis_elegans.PRJNA13758.WBPS19.orthologs.tsv.gz" rel="nofollow noreferrer">TSV files</a> for each genome on wormbase via <a href="https://parasite.wormbase.org/ftp.html" rel="nofollow noreferrer">parasite</a>. My suggestion would be to map those to your expression matrix files and use them to merge datasets using your favorite method in python or R.</p>
<p>Granted, wormbase seems to be going through a gap in funding so some of their services may be down. I had some difficulty clicking around in their comparator genomes.</p>
<p>Alternatively, you might be evaluating expression based on the N2 reference. (Not that this would be ideal.) In this case there would be no issue of orthology, because there would only be one genome/transcriptome assembly.</p>
<p>Failing all of this, you could use <a href="https://www.science.org/doi/10.1126/science.abn3107" rel="nofollow noreferrer">one of various tools</a> (<a href="https://academic.oup.com/bioinformatics/article/37/12/1639/6035128" rel="nofollow noreferrer">here is another option</a>) to annotate any C. elegans assembly with respect to a high quality reference such as N2.</p>

CC BY-SA 4.0
2024-12-26T22:37:10.030Z
Thanks!! This info is helpful, but let me clarify about the other thing!!
eshaan
CC BY-SA 4.0
2024-12-27T03:06:06.113Z
Maybe @eshaan mark the question as "resolved" and ask a new question? That is the etiquette approach on the site.
M__
CC BY-SA 4.0
2024-12-26T15:46:35.590Z
2024-12-26T15:46:35.590Z
Maximilian Press
<p>I am working with doing RNA seq analysis in different strains of C elegans. I wanted to ask if the orthologous genes were given the same name for reference genomes for different strains on WormBase. That would make my life easier as I could compare the expression across strains for the common genes.</p>
<p>By &quot;name&quot; I meant the identifier, like WBGene00067890.</p>
<p>If this is not so, could you please suggest how I can get same gene identifiers for orthologous genes?</p>
<p>Thanks a lot.</p>

CC BY-SA 4.0
2024-12-26T22:20:16.517Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
<rna-seq><reference-genome><gtf><wormbase>
Are the Gene names in genome annotations for GTFs of C elegans strains given on WormBase consistent?
# Are the Gene names in genome annotations for GTFs of C elegans strains given on WormBase consistent?

(Asked by: username_0 on 2024-12-26)

I am working with doing RNA seq analysis in different strains of C elegans. I wanted to ask if the orthologous genes were given the same name for reference genomes for different strains on WormBase. That would make my life easier as I could compare the expression across strains for the common genes.

By "name" I meant the identifier, like WBGene00067890.

If this is not so, could you please suggest how I can get same gene identifiers for orthologous genes?

Thanks a lot.

**Tags:** rna-seq, reference-genome, gtf, wormbase
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  

---

## 1 answers

### Answer by username_2 on 2024-12-26. Score: 1

It would be helpful to know

1. what you mean by "name"- like a non-systematic gene symbol ("P53") or a systematic identifier ("NP\_000537.1")?
2. exactly which strains you are working with. Wormbase does not seem to have very many diverse genome assemblies for C. elegans readily available. (Note that I am not a worm/wormbase person, maybe I'm missing something.)

But gene orthology for the main genomes is given directly in [TSV files](https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS19/species/caenorhabditis_elegans/PRJNA13758/caenorhabditis_elegans.PRJNA13758.WBPS19.orthologs.tsv.gz) for each genome on wormbase via [parasite](https://parasite.wormbase.org/ftp.html). My suggestion would be to map those to your expression matrix files and use them to merge datasets using your favorite method in python or R.

Granted, wormbase seems to be going through a gap in funding so some of their services may be down. I had some difficulty clicking around in their comparator genomes.

Alternatively, you might be evaluating expression based on the N2 reference. (Not that this would be ideal.) In this case there would be no issue of orthology, because there would only be one genome/transcriptome assembly.

Failing all of this, you could use [one of various tools](https://www.science.org/doi/10.1126/science.abn3107) ([here is another option](https://academic.oup.com/bioinformatics/article/37/12/1639/6035128)) to annotate any C. elegans assembly with respect to a high quality reference such as N2.

> **Comments:**
> **username_0**: Thanks!! This info is helpful, but let me clarify about the other thing!!  
> **username_3**: Maybe @eshaan mark the question as "resolved" and ask a new question? That is the etiquette approach on the site.  

---

