-ptf option - recommended input & implementation details?

[SamBryce-Smith]

Hi,

I'm interested in using StringTie finding novel last exons and the recently added -ptf option seems quite relevant. I have a couple of questions regarding recommended input sites and also how these sites are incorporated into the assembly algorithm (as somewhat related I thought I'd keep to one issue).

1. Is recommended annotation a complete set of coordinates (e.g. the whole PolyASite database or Gencode manual poly(A) feature annotation), like passing the whole reference transcript annotation to -G, or was it designed with experiment-specific/parallel sequencing data in mind (e.g. 3'-end sequencing from the same samples)?

2. How are these coordinates used to refine the starts/ends of predicted exons? I don't see anything in the documentation or the release notes (& don't expect it in paper as option was first available April 2020 in v2.1.2).

Thanks for your time and for development and support of StringTie!

All the best, Sam