Read counts doubt

[Miriam Martínez]

Hi and Happy New Year,

I had a doubt regarding the clasification of the types of read. I have explored the splicegraph.sql file, and I have seen that the reads are classified in junction reads and intron retention reads basically. I want to use the reads to calculate like an "intron retention rate" of my data, so I looked up for the classification of each read on the paper "RNA splicing analysis using heterogeneous and large RNA-seq dataset". In there I have found how they are classified, but the reads that include part of the exon and the start/end of the intron, I don't actually understand its classification, as it says: "If the intron start is contained in the aligned read, the intron “position” is defined as for junctions (treating the exon/intron boundary as a junction with zero length).". In order to understand it, I attach an image with a simple example of the types of reads and I was wondering if you could help me out to understand how the types of reads are classified when saving the data on the .sql file. Using the image as reference:

- Blue: junction read

- Orange: neither

- Purple: intron retention read

- Green: ???

Thank you very much in advance for your help!

Best,

Miriam