Hi all:

I have been doing analysis on RNA-seq data. I have a file containing the coordinates of the intron. I have converted them into bed files. I also have generated bed files from GTF files. My aim is to calculate the distribution of introns across the transcript: 5UTR/CDS/3UTR. However, I noticed that in the GTF generated bed files for UTR and CDS. the coordinates are all for exons.

I am wondering under such circumstances, what is the solution to do intersect? Theoretically, I will get zero overlap.

Thanks,