I merged 93 samples with StringTie merge. Most of the isoforms were merged well, but when there is another isoform with another exon on the 5' side (in the example below, there are 3 exons in S1 and 2 exons in S17), the isoform with 2 exons is erased by merge even if the expression level is high. I have to edit the annotation manually. Is there any way to solve this problem?
I merged 93 samples with StringTie merge. Most of the isoforms were merged well, but when there is another isoform with another exon on the 5' side (in the example below, there are 3 exons in S1 and 2 exons in S17), the isoform with 2 exons is erased by merge even if the expression level is high. I have to edit the annotation manually. Is there any way to solve this problem?