Differential Expression analysis of Brassica polyploids

Question

[thulani.m.hewavithana]

Hello, I'm having a problem in the Differential Expression analysis of Brassica allopolyploids. I have sequenced paired end read data from three Brassica diploids and three Brassica tetraploids. I have aligned them separately to the reference genome and expression quantification was done using RSEM. But I don't understand how can I do the Differential Expression analysis between diploids and tetraploids. Because they have different gene id's in their count tables. Please help me to clarify this problem!

Thanks in advance.