I am new to bioinformatics and have a question for my project. I have three species that have close relationships, one species has a reference genome (I used hisat2 for this), other two species haven't had a reference genome, each species have about 7 time-point. I assembly the two species without reference genome using de-novo trinity method. But I just confused about what I need to do the next step? do I need to make a gtf file using transcriptome and mapped reads to the transcriptome, just like what I did for the species that have a genome? My goal is to find the differential expression genes and find the key-genes that related to our project.
I would be really appreciated if you could give me any suggestions.