I want to do differential expression analysis with DESEQ2. I have three read counts files downloaded from GEO (small RNAseq based) where the number of miRNAs and id is nearly the same. These studies have used the same tool for alignment but different tools for counting aligned reads.
My question is
- Can I combine these read count files
- Is there any recommended meta-analysis based tool for this purpose
- Is there any other way to do this other then redoing RNA-seq analysis.