I'm using hisat2, stringtie tools for the RNA-Seq analysis. After stringtie using ballgown I get FPKM and TPM values for every gene.
I have seen that edgeR, Deseq2 can be used for Counts data. I would like to know which R package needs to be used for differential analysis with TPM values?
Which one is better for differential analysis FPKM or TPM?