Dear Developer:
I read several papers on analyzing intron retention. I would like to know if you can share the calculating standard on deciding intron retention used by ASpli.
For example: the output E1i.counts and IE2.counts are the same with the junction1, and junction 2. That is very convenient. However, I found that when deciding if a intron is retained people will use a different standard. For example, in the paper https://genome.cshlp.org/content/24/11/1774.full.pdf+html, in page 10 the author explained their way to analyze intron retention, which I found convincing.
In one word, is it possible for you to add the statistical standard on the results?
Dear Developer: I read several papers on analyzing intron retention. I would like to know if you can share the calculating standard on deciding intron retention used by ASpli. For example: the output E1i.counts and IE2.counts are the same with the junction1, and junction 2. That is very convenient. However, I found that when deciding if a intron is retained people will use a different standard. For example, in the paper https://genome.cshlp.org/content/24/11/1774.full.pdf+html, in page 10 the author explained their way to analyze intron retention, which I found convincing.
In one word, is it possible for you to add the statistical standard on the results?
Many thanks,
Cai