usually retained introns

Question

[adi.gershon1]

Hi I'm doing an analysis of intron retention. i wanted to calculate intron length of the interim I found retained in my analysis and compare them to intron that are usually retained. but I'm having problems figuring out how to find the characteristics of introns usually retained can someone help me (Human)?

[Eric Lim]

Usually retained can be defined in many ways. The lowest-hanging fruit is probably annotated intron retentions found in GTFs. You can parse the GTF or use splicing tools like SUPPA2 (https://github.com/comprna/SUPPA) to generate a list of retained introns from a GTF. Then go from there