Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-30T22:30:28.247Z
Comments.Text: 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
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-30T22:33:11.690Z
Comments.Text: 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
Comments.UserDisplayName: StupidWolf
Tags: <rna-seq><gene-expression>
Title: How to convert Illumina IDs to Gene Names?
ThreadText: # 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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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  
  
  ---
  
  ## 0 answers
  
  