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:

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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.


1 Answer 1


You have a few options:

  1. Downsample the fastq files and rerun the entire analysis. You can do this with seqtk sample.
  2. Downsample the BAM files, which you can do with samtools view -s.
  3. 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.

  • $\begingroup$ thanks for the reply @Devon Ryan, Yes, I feel that the 3rd option is much easier. To use the 2nd option, I have to mention that the raw read counts of the transcripts were extracted from the stringtie step using prepDE.py python script [ccb.jhu.edu/software/stringtie/index.shtml?t=manual] Will there be any problem? $\endgroup$ Apr 24, 2020 at 9:32
  • $\begingroup$ I don't use stringTie, so I can't comment with certainty. $\endgroup$
    – Devon Ryan
    Apr 24, 2020 at 9:34
  • $\begingroup$ ok. And if I have to use the 2nd option, Is this right? samtools view -s number GroupA_12.bam > GroupA_12_new.bam What I should give the fixed number for downsampling? $\endgroup$ Apr 24, 2020 at 9:49
  • 1
    $\begingroup$ If you need 20% then 1234.2. 1234 is just a seed for reproducibility, .2 is the fraction to keep. $\endgroup$
    – Devon Ryan
    Apr 24, 2020 at 9:51
  • $\begingroup$ Small question. How to decide the fraction of reads to keep? I mean 0.2 or 0.5 or something else? On what basis I should give the fraction? $\endgroup$ Apr 25, 2020 at 22:22

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