I'm going to assume your organism has a reference genome, otherwise this is a different question all together. From a scan of the Trinity documentation, it looks like it gives you the assembled fasta sequences of your genes and transcripts. So to find the exon-exon junctions, you're going to need to compare your transcript sequences to your reference organism's sequence. Try using something like BLAT to align your transcripts (https://genome.ucsc.edu/cgi-bin/hgBlat), which will give you the coordinates that each "exon" maps to. Depending on how many transcripts you need to do this for, you may need to run the command-line version of BLAT, then convert the output to something like BED format, assuming you need to visualise your transcript exon boundaries.