Hi:
Recently I analyzed the Encode RNA-seq data using ASpli. I would like to get some insight of how the intron retention changed during neural differentiation. I have sone questions on the output files:
The intron I am interested is part of an exon in another transcript. So it is not an output in the "Intron"file, instead, it is in the junction file. The current situation is that: I want to use a filter standard to filter out similar genes. But in the junction file there is no intronic reads. Usually when we filtering intron retention events we use reads from J1, J2, J3 and #I to calculate.
Hi: Recently I analyzed the Encode RNA-seq data using ASpli. I would like to get some insight of how the intron retention changed during neural differentiation. I have sone questions on the output files: The intron I am interested is part of an exon in another transcript. So it is not an output in the "Intron"file, instead, it is in the junction file. The current situation is that: I want to use a filter standard to filter out similar genes. But in the junction file there is no intronic reads. Usually when we filtering intron retention events we use reads from J1, J2, J3 and #I to calculate.
I hope there is some response after my post.
Cai