Hello!

Does someone know a way to predict the NMD targets from the long read datasets? Ideally, it should be a ready tool.

I found the next way to do it in an article:

To determine whether an AS event generated an isoform that contains premature stop codons and could be degraded by NMD, we first predicted the longest ORF of each isoform by EMBOSS (Rice et al. 2000) and then calculated the distance between the stop codon and the last exon junction for each isoform. If one isoform had a distance >50 nt whereas the other had a distance <50 nt, then the AS event was regarded as producing an NMD candidate (Wang and Brendel 2006)

It was used in some other articles as well. But if I try to follow it, it will take just a lot of time, because I'm quite new in bioinformatics.

Another possibility is "NMD Classifier", but I have not found any links that it can be used with the Pacbio data.

Any help will be highly appreciated.