once you have mapped the data against the genome of your interest, you can simply use FeatureCounts program for instance:
featureCounts -a yourGTF.gtf -t UTR5 -g transcript_id -o counts_UTR5_transcripts.txt
The -t option allows you to select a type of features to be counted.
The -g option allows you to choose "how to group your data". Using transcript_id (or something equivalent in your GTF/GFF), you tell to FeatureCounts: "ouput the counts for each transcript".