Extracting 3' UTR from long read RNA sequencing reads

Question

[peris]

Hi All,

I am having a question regarding long read sequencing. I have sequenced my samples using long read sequencing technology. I have identified multiple isoforms from the data and many of them are with alternative last exons. I have the gtf file of the isofroms. Now, I want to extract the 3' UTR sequences and also want to study its usage among different condition. Since its a long reads, my coverage is not that great. In such scenario what will be the best tool to extract the 3' UTRs and also study its usage among samples.

Thanks