text: user1377: I have 40 samples and these are into two groups. I would like to perform a differential analysis between two groups. The library size of the samples is very low. But there are two samples (GroupA_12 and GroupB_2) in which the number of counts is too large compared to other samples. Please check the library sizes below:
  
  I wanted to downsample these two cases and then would like to perform differential analysis. May I know how to downsample those two samples. 
  Any help is appreciated. thanq.
  
  user77: You have a few options:
  
  Downsample the fastq files and rerun the entire analysis. You can do this with seqtk sample.
  Downsample the BAM files, which you can do with samtools view -s.
  Divide all of the counts in the counts files by some factor and round that to an integer.
  
  I personally prefer option 2, since it's quick and doesn't usually have any side-effects unless you use two-pass alignment or did the quantification with something like salmon. Option 3 is always tempting, but I have to say I've never been convinced that this consistently produces similar enough results to options 1 or 2. 
  
original_text: 1377: <p>I have 40 samples and these are into two groups. I would like to perform a differential analysis between two groups. The library size of the samples is very low. But there are two samples (GroupA_12 and GroupB_2) in which the number of counts is too large compared to other samples. Please check the library sizes below:</p>
  
  <p><a href="https://i.stack.imgur.com/eI2m8.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/eI2m8.png" alt="enter image description here"></a></p>
  
  <p>I wanted to downsample these two cases and then would like to perform differential analysis. May I know how to downsample those two samples. </p>
  
  <p>Any help is appreciated. thanq.</p>
   77: <p>You have a few options:</p>
  
  <ol>
  <li>Downsample the fastq files and rerun the entire analysis. You can do this with <code>seqtk sample</code>.</li>
  <li>Downsample the BAM files, which you can do with <code>samtools view -s</code>.</li>
  <li>Divide all of the counts in the counts files by some factor and round that to an integer.</li>
  </ol>
  
  <p>I personally prefer option 2, since it's quick and doesn't usually have any side-effects unless you use two-pass alignment or did the quantification with something like salmon. Option 3 is always tempting, but I have to say I've never been convinced that this consistently produces similar enough results to options 1 or 2. </p>
  