I was reading this post and wondering what could be the best tool to perform meta-analysis for RNA-seq experiment. Is DESeq2 a good tool for that? I have heard about metaSeq and it seems to be good. Any experience with the latter, by any chance?
another question is whether meta analysis could be done for comparing different cell types that have the same genotype. For example, same KO cells (compared to wt) isolated from different tissues, each gathered from ≠ labs?