rnabioco / mzt-introns Goto Github PK

hello, I try to repeat your analysis. It's a good project which makes a nearly newbie could finish it. And I found that in the pipeline the intronic signal will be allocated to only one transcript if there're more than one transcripts(eg. there are two transcripts A,B that have the same intron, then only A or only B has intronic signal ). Is this will affect the downstream analysis in transcript-level?
And I noticed that in your paper when you do transcript isoform analysis, first we find the significant genes, then we select the representative maternal or zygotic isoform respectively. If there're more than one isoforms, will it be ignored it ? Why not directly find the significant transcript isoform?