I have 30 FASTQ files that I used to create a de novo transcriptome in Trinity. I then aligned the reads back to the assembly using RSEM. This is an organism that does not have an annotated genome. Is it possible to use DESeq and upload my data via tximport? I have a text file with the URL to each recults folder but I am not sure how to import them.
The short answer is yes. One would assume that you read all the documentation that comes with Trinity, including say this page? Which tells you things about the output that might be important for you when you are thinking about using tximport.
If you haven't closely read the Trinity documentation, then you should probably do so. Trying to do something complicated without having exposed yourself to the complexities of what you are trying to do is suboptimal.