Answers.Body: <p>Either of the first two columns are fine to use, though I personally prefer the "intersectionNotEmpty" one.</p>
  
  <p>As an aside, that looks like a custom format file produced from post-processing htseq-count output.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-01T08:35:05.233Z
Answers.LastActivityDate: 2020-03-01T08:35:05.233Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information</p>
  
  <pre><code>                  readcounts_union  readcounts_intersectionNotEmpt  genelength  R/FPKM_union    R/FPKM_intersectionNotEmpt
  ENSG00000000003.10             8                      8               3688     1.06120392730222        1.05722142116966
  
  ENSG00000000419.8             31                     31               4032     3.76132572546529               3.74721015127372
  </code></pre>
  
  <p>People say</p>
  
  <pre><code>readcounts_union
  </code></pre>
  
  <p><strong><em>reads that overlap a single feature are included in the count for that feature; reads that overlap more than one feature are not included in the counts</em></strong></p>
  
  <pre><code>readcounts_intersectionNotEmpty
  </code></pre>
  
  <p><strong><em>regions that are shared between features are excluded; reads that overlap a remaining region are included in the count for the feature that includes that region; reads that overlap regions from more than one feature are not included in the counts</em></strong></p>
  
  <pre><code>R/FPKM_union
  </code></pre>
  
  <p><strong><em>readcounts_union normalised for gene length and sequencing depth</em></strong></p>
  
  <pre><code>R/FPKM_intersectionNotEmpty
  </code></pre>
  
  <p><strong><em>readcounts_intersectionNotEmpty normalised for gene length and sequencing depth</em></strong></p>
  
  <p>I want to do differential expression analysis between groups but I don't know which column I should use for DESeq2</p>
  
  <p>Anybody familiar with such a format?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-01T05:54:58.170Z
Comments.Text: I've never seen this format before, what program generated this file? DESeq2 requires raw counts as input (it does it's own normalization internally), so you should avoid using the FPKM values with DESeq2
Comments.UserDisplayName: Tomas Bencomo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-02T20:04:58.713Z
Comments.Text: I don't have access to the raw files, I rather have been given only this format and been asked to give them list of differentially expressed genes
Comments.UserDisplayName: Zizogolu
Tags: <r><rna-seq><differential-expression><deseq2><normalization>
Title: How are these definitions related to differential expression?
ThreadText: # How are these definitions related to differential expression?
  
  (Asked by: username_0 on 2020-03-01)
  
  I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information
  
  ```
                    readcounts_union  readcounts_intersectionNotEmpt  genelength  R/FPKM_union    R/FPKM_intersectionNotEmpt
  ENSG00000000003.10             8                      8               3688     1.06120392730222        1.05722142116966
  
  ENSG00000000419.8             31                     31               4032     3.76132572546529               3.74721015127372
  
  ```
  
  People say
  
  ```
  readcounts_union
  
  ```
  
  ***reads that overlap a single feature are included in the count for that feature; reads that overlap more than one feature are not included in the counts***
  
  ```
  readcounts_intersectionNotEmpty
  
  ```
  
  ***regions that are shared between features are excluded; reads that overlap a remaining region are included in the count for the feature that includes that region; reads that overlap regions from more than one feature are not included in the counts***
  
  ```
  R/FPKM_union
  
  ```
  
  ***readcounts\_union normalised for gene length and sequencing depth***
  
  ```
  R/FPKM_intersectionNotEmpty
  
  ```
  
  ***readcounts\_intersectionNotEmpty normalised for gene length and sequencing depth***
  
  I want to do differential expression analysis between groups but I don't know which column I should use for DESeq2
  
  Anybody familiar with such a format?
  
  **Tags:** r, rna-seq, differential-expression, deseq2, normalization
  
  > **Comments:**
  > **username_1**: I've never seen this format before, what program generated this file? DESeq2 requires raw counts as input (it does it's own normalization internally), so you should avoid using the FPKM values with DESeq2  
  > **username_0**: I don't have access to the raw files, I rather have been given only this format and been asked to give them list of differentially expressed genes  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-03-01. Score: 2 | Accepted answer
  
  Either of the first two columns are fine to use, though I personally prefer the "intersectionNotEmpty" one.
  
  As an aside, that looks like a custom format file produced from post-processing htseq-count output.
  
  
  ---
  
  