I am trying to figure out the best way to make a list of genes that are differentially expressed after gene knockdown. RNAseq was done on a set of samples, about 30million reads/sample. 270 million total reads. I mapped the reads to transcriptome #1 and made a list of candidate genes FC <2, p-val<0.05. This resulted in a list of 286 genes. I did the same thing for transcriptome #2 resulting in a list of 315 genes. Both transcriptomes are from two different labs but are on the same wildtype animal. I expected that the two resulting lists would have been very similar. However, when I compared those two lists and only about 1/3 of the genes were the same between the two. Is there any reason why this might be?