<p>I am new to the area of bioinformatics, so apologies if this is too obvious of a query.</p>
<p>I need to analyze the RNA Seq data from <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98455" rel="nofollow noreferrer">GSE98455</a>.</p>
<p>The dataset is of the following format:</p>
<pre><code>|---------------------|------------------|
|    Some Id          |      Counts      | 
|---------------------|------------------|
|    13101.t00001     |       392        |
|---------------------|------------------|
|    13101.t00002     |        20        |
|---------------------|------------------|
</code></pre>
<p>I would like to extract the counts for certain genes only. So how do I match the ID column with gene names? Is there a reference table or something I need to look at?</p>
<p>Side Note: Usually for microarray data, I refer to the GPL files which provide a reference between accession ID and Gene Names. I was not able to do that for this RNA Seq Data set.</p>
<p>Update May 2, 2020: I reached out to the authors earlier today. I looked at the paper associated with this dataset, it seems the annotation belongs to <em>Oryza sativa japonica</em> reference genome v 6. I can't find anything related to it on the web. If I get any response from the authors, I will update it here.</p>

CC BY-SA 4.0
2020-04-30T22:30:28.247Z
you have to ask the authors. I checked https://plants.ensembl.org/Oryza_sativa/Info/Index?db=core and the gffs don't have any transcripts that match it
StupidWolf
CC BY-SA 4.0
2020-04-30T22:33:11.690Z
This is not illumina IDs. you can read the data processing, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2596386, they aligned it to the ensembl genome and i have no idea what annotation is used
StupidWolf
<rna-seq><gene-expression>
How to convert Illumina IDs to Gene Names?
# How to convert Illumina IDs to Gene Names?

(Asked by: username_0 on 2020-04-30)

I am new to the area of bioinformatics, so apologies if this is too obvious of a query.
I need to analyze the RNA Seq data from GSE98455.
The dataset is of the following format:
|---------------------|------------------|
|    Some Id          |      Counts      | 
|---------------------|------------------|
|    13101.t00001     |       392        |
|---------------------|------------------|
|    13101.t00002     |        20        |
|---------------------|------------------|

I would like to extract the counts for certain genes only. So how do I match the ID column with gene names? Is there a reference table or something I need to look at?
Side Note: Usually for microarray data, I refer to the GPL files which provide a reference between accession ID and Gene Names. I was not able to do that for this RNA Seq Data set.
Update May 2, 2020: I reached out to the authors earlier today. I looked at the paper associated with this dataset, it seems the annotation belongs to Oryza sativa japonica reference genome v 6. I can't find anything related to it on the web. If I get any response from the authors, I will update it here.

**Tags:** rna-seq, gene-expression
> **Comments:**
> **username_1**: you have to ask the authors. I checked https://plants.ensembl.org/Oryza_sativa/Info/Index?db=core and the gffs don't have any transcripts that match it  
> **username_1**: This is not illumina IDs. you can read the data processing, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2596386, they aligned it to the ensembl genome and i have no idea what annotation is used  

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## 0 answers

