Answers.Body: <p>It's safer to import everything.  You'll want all the data for normalization and dispersion estimates.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-16T18:58:17.633Z
Answers.LastActivityDate: 2021-02-16T18:58:17.633Z
Answers.UserDisplayName: swbarnes2
Body: <p>I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of reads per sample. If I only input a subset of all the transcripts, the sequencing depth will change.</p>
  <p>So my question is: can I simply input the subset of interest? Or should I input all transcripts, and subset the results later?</p>
  
Tags: <deseq2><normalization><subset>
Title: Differential expression analysis for a subset of transcripts
ThreadText: # Differential expression analysis for a subset of transcripts
  
  (Asked by: username_0 on 2021-02-16)
  
  I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of reads per sample. If I only input a subset of all the transcripts, the sequencing depth will change.
  
  So my question is: can I simply input the subset of interest? Or should I input all transcripts, and subset the results later?
  
  **Tags:** deseq2, normalization, subset
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-02-16. Score: 3 | Accepted answer
  
  It's safer to import everything. You'll want all the data for normalization and dispersion estimates.
  
  
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