why iso1 subsumed by iso2 doesn't need the same exons number?

[zhangfei1947]

Dear TAPIS developer: if read1 subsumed by read2 then the read1 would not added as an isoform, but subsumedIso() allow read1's exons number less than read2's, I want to know why.

[Mike Hamilton]

This is because of the nature of poly-A selection and how the primers are designed. If a read is subsumed by another, with matching 3'-most splice junctions, we cannot say that it is a new isoform because it is possible that the smaller read is only part of the isoform. To be sure that it really is a new isoform, 5' capture techniques would be necessary.