<p>The tutorial you linked to does not mention ERCC or mt genes.</p>

<p>Before running <code>grepl</code> or any other search, you should first check your inputs. It looks like you have WormBase gene IDs if all your genes look like <code>WBGene00023193</code>. Therefore, your question is actually how to convert WormBase gene IDs to gene symbols.</p>

<p>Here is one potential solution: <a href="https://github.com/WormBase/website/issues/4297" rel="nofollow noreferrer">https://github.com/WormBase/website/issues/4297</a></p>

<p>After you convert, you have to make sure that you have ERCC spike-ins in your gene table (probably not) and you mitochondrial genes start with "mt-".</p>

CC BY-SA 3.0
2017-12-13T18:54:33.737Z
Sorry about that, the link was wrong. I updated it
Nikita Vlasenko
CC BY-SA 3.0
2017-12-13T18:27:49.483Z
2017-12-13T18:37:47.017Z
2017-12-13T18:37:47.017Z
burger
<p>I am having <code>RNA-seq</code> data set for <code>C.Elegans</code>. I do not know which annotation scientists used for naming the genes of it, but I need to search somehow for the <code>^ERCC</code> and <code>^mt-</code> genes like specified in the tutorial:</p>

<p><a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" rel="nofollow noreferrer">https://www.bioconductor.org/help/workflows/simpleSingleCell/</a></p>

<p>If I just implement <code>grepl</code> search for the <code>character</code> array of gene names that I have, I am always getting all values <code>FALSE</code> as if there are no <code>spike-in</code>s and mitochindrial genes.</p>

<p>Any suggestion would be greatly appreciated.</p>

<p>Sample gene name from the dataset: <code>WBGene00023193</code></p>

<rna-seq><gene>
Get gene annotation type from gene name
# Get gene annotation type from gene name

(Asked by: username_0 on 2017-12-13)

I am having `RNA-seq` data set for `C.Elegans`. I do not know which annotation scientists used for naming the genes of it, but I need to search somehow for the `^ERCC` and `^mt-` genes like specified in the tutorial:

<https://www.bioconductor.org/help/workflows/simpleSingleCell/>

If I just implement `grepl` search for the `character` array of gene names that I have, I am always getting all values `FALSE` as if there are no `spike-in`s and mitochindrial genes.

Any suggestion would be greatly appreciated.

Sample gene name from the dataset: `WBGene00023193`

**Tags:** rna-seq, gene

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## 1 answers

### Answer by username_1 on 2017-12-13. Score: 2 | Accepted answer

The tutorial you linked to does not mention ERCC or mt genes.

Before running `grepl` or any other search, you should first check your inputs. It looks like you have WormBase gene IDs if all your genes look like `WBGene00023193`. Therefore, your question is actually how to convert WormBase gene IDs to gene symbols.

Here is one potential solution: <https://github.com/WormBase/website/issues/4297>

After you convert, you have to make sure that you have ERCC spike-ins in your gene table (probably not) and you mitochondrial genes start with "mt-".

> **Comments:**
> **username_0**: Sorry about that, the link was wrong. I updated it  

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