Mapping reads against a de novo assembly -- no genome available

Question

[Lucila]

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.

Best, Lucila.

Answer 1

[Mehmet]

Please have a look.

Question: Mapping onto the Transcriptome, RNA-seq