Hi all, I have assembled a de novo transcriptome with Trinity and I was wondering which is the best approach to assess the differential expression of my samples. I have 2 conditions, with 4 replicates each, it means a total of 8 libraries with paired end reads that I used to make the assembly. I do not have an available genome from my organism. Can I use STAR to map the reads against the de novo assembly? Or do you recommend another approach to obtain the reads per each transcript? Any suggestions are welcome.