Answers.Body: <p>To filter your gene_exp.diff either you export it to excel and then filter because it is columns separated by tabs or use the command (awk and head -n) to filter and have the number of lines you want if you master Linux</p>
  
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Answers.CreationDate: 2020-04-22T01:00:35.967Z
Answers.LastActivityDate: 2020-04-22T01:00:35.967Z
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Body: <p><em>This question has also been asked on <a href="https://www.biostars.org/p/428956/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>I have run <em><strong>cuffdiff</strong></em> (with statistics turned ON) to compare two groups of samples: <em>Control group</em> and <em>Late AD group</em>.</p>
  <p>This is the command I ran to be precise:</p>
  <pre><code>cuffdiff -L Control,AD_Late_Braak -p 8 --total-hits-norm --frag-bias-correct ../References/ensembl.GRCh38.99.fa --multi-read-correct --library-norm-method quartile ../References/Homo_sapiens.GRCh38.99.chr.gtf Early_Braak_Control_1,Early_Braak_Control_2,Early_Braak_Control_3 Late_Braak_Sample_1,Late_Braak_Sample_2,Late_Braak_Sample_3
  </code></pre>
  <p>I'm looking at the output from <em>cuffdiff</em> and I see a <em><strong>gene_exp.diff</strong></em> file which contains the results of the differential expression testing. I want to know what is the best way to filter the results of this gene_exp.diff file so as to restrict the number of genes that are up-regulated and down-regulated to a list between ~50-850.</p>
  <p>P.S My thoughts are to tweak the <strong>p-values</strong> and <strong>log2 fold change</strong> values, but seems like a trail-and-error method, so I was wondering if there was a more &quot;formal&quot; method/approach?</p>
  
Tags: <rna-seq><differential-expression>
Title: Filtering genes from cuffdiff results
ThreadText: # Filtering genes from cuffdiff results
  
  (Asked by: username_0 on 2020-03-25)
  
  *This question has also been asked on [Biostars](https://www.biostars.org/p/428956/)*
  
  I have run ***cuffdiff*** (with statistics turned ON) to compare two groups of samples: *Control group* and *Late AD group*.
  
  This is the command I ran to be precise:
  
  ```
  cuffdiff -L Control,AD_Late_Braak -p 8 --total-hits-norm --frag-bias-correct ../References/ensembl.GRCh38.99.fa --multi-read-correct --library-norm-method quartile ../References/Homo_sapiens.GRCh38.99.chr.gtf Early_Braak_Control_1,Early_Braak_Control_2,Early_Braak_Control_3 Late_Braak_Sample_1,Late_Braak_Sample_2,Late_Braak_Sample_3
  
  ```
  
  I'm looking at the output from *cuffdiff* and I see a ***gene\_exp.diff*** file which contains the results of the differential expression testing. I want to know what is the best way to filter the results of this gene\_exp.diff file so as to restrict the number of genes that are up-regulated and down-regulated to a list between ~50-850.
  
  P.S My thoughts are to tweak the **p-values** and **log2 fold change** values, but seems like a trail-and-error method, so I was wondering if there was a more "formal" method/approach?
  
  **Tags:** rna-seq, differential-expression
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-04-22. Score: 1
  
  To filter your gene\_exp.diff either you export it to excel and then filter because it is columns separated by tabs or use the command (awk and head -n) to filter and have the number of lines you want if you master Linux
  
  
  ---
  
  