Quantify a sample with two different annotations will generate different results on their common transcripts in the two annotations

[dudududu12138]

Hi, I have a new question about your discussions in #249. I have two reference annotations A and B and they share most common transcripts while they also have some private transcripts. Then I ran reference based quantification with the two annotations separately(input the same bam file). Will the quantification results be same between the common transcripts both in A and B?

[andrewprzh]

Dear @dudududu12138

In general, I'd say no.
For example, say we have a gene, for which annotation A has 3 isoforms I1 I2 I3 and annotation B has 1 extra isoform I4. Let's say this extra isoform I4 is quite similar to one of the 3 common isoforms, let's say I1. Then, it can happen that some of the reads will be uniquely assigned to I1 when using A, but when using B, the algorithm won't be able to unambiguously choose between I1 and I4, thus making these reads as ambiguous. This will result in different quantification results.

Best
Andrey

[dudududu12138]

Thanks!