text: user6477: 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?
  
  user2388: It's safer to import everything.  You'll want all the data for normalization and dispersion estimates.
  
original_text: 6477: <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>
   2388: <p>It's safer to import everything.  You'll want all the data for normalization and dispersion estimates.</p>
  