Comments (2)
Hi Rachel,
unfortunately the current version of ASGAL cannot detect that kind of intron retention. Indeed, ASGAL aligns reads to the splicing graph (in other words to the known exons of a gene): in your case, there are a lot of reads mapping to an intron (as you can see from the coverage plot).
In the paper we said:
We note that the current implementation of ASGAL is not able to detect the insertion of novel exons inside an intron and intron retention events caused by the union of two exons
Your case is exactly the second one we mentioned. Maybe it isn't clear enough: in case, sorry for that.
Best,
Luca
from galig.
Hi Luca,
OK, thanks for clarifying that.
Best,
Rachel
from galig.
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