text: user4595: 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?
  
  user77: 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.
  
original_text: 4595: <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>
   77: <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>
  