text: user12203: I am doing an RNAseq experiment with affected (n=6) and control groups (n=6) in cow. However it turned out that 4 of my control samples have very low quality so I have to discard them.
  My problem is that there is no way to repeat the sampling and sequencing.
  Are there any solutions to perform DE,GSEA with these conditions (somehow generating bootstrapped samples from control groups or something similar)?
  Thanks in advance!
  
  user-1: There is no obstacle in performing a DE analysis and all downstream on a 6 vs 2 comparison. The only thing to keep in mind is that the representation of the control is not particularily good, but you can technically perform the exact same analysis as if it was 6 vs 6, e.g. with DESeq2, edgeR or limma-voom/trend.
  
original_text: 12203: <p>I am doing an RNAseq experiment with affected (n=6) and control groups (n=6) in cow. However it turned out that 4 of my control samples have very low quality so I have to discard them.
  My problem is that there is no way to repeat the sampling and sequencing.
  Are there any solutions to perform DE,GSEA with these conditions (somehow generating bootstrapped samples from control groups or something similar)?
  Thanks in advance!</p>
   -1: <p>There is no obstacle in performing a DE analysis and all downstream on a 6 vs 2 comparison. The only thing to keep in mind is that the representation of the control is not particularily good, but you can technically perform the exact same analysis as if it was 6 vs 6, e.g. with DESeq2, edgeR or limma-voom/trend.</p>
  