I have four transcriptome assembly of the same species but with different treatments . I want to annotate each of transcriptome assembly to closely related reference cDNA species (from ensembl). Then I want to compare each of the annotated transcriptome assembly and to see how many genes appear.
I want to know which genes present in all treatments and what are all the genes that are absent in different treatments. I have tried tblastx with ensembl (cDNA) sequence against transcriptome assemblies.Trying to find out genes which having highest blast coverage.I would like to get idea to better way to compare to get list of genes. Any journal paper info regarding this will be helpful.