We have sequenced from two tissue of plants which are distantly related but are from same species. I want to compare these two transcriptome of these two plants and to find novel genes by comparing two transcriptomes. How can I do that?. Any suggestions?.
I am thinking on the workflow
1. Denovo assembling of two plant transcriptome separately
2. Do gene expression analysis for these denovo assembled plants separately
3. Find novel overlapping genes of these plants.
Is this workflow is correct, please correct me if I am wrong.