I am currently working on analysis of TIF-seq (Transcript isoform sequencing) data. In brief, TIF-seq allows the identification of transcript isoforms by selective sequencing of full-length mRNA molecules with 5'caps and poly(A) tails. As part of the analysis, I am interested in mapping transcription start sites (TSS) clusters and Poly(A) sites (PAS) clusters based on the sequencing reads, in order to define transcription isoforms boundaries. I am aware that several tools to analyze (and particularly cluster) TSS data (CAGEr, CAGEfightR, icetea, TSRchitect, TSRexploreR and TSSr) are available. However, I was not able to find tools to cluster PAS data. I would be very thankful for any assistance in finding such tools, or perhaps guidance in adaptation of the existing TSS tools to handle PAS data (as far as I am aware, the TSS tools are uniquely developed to handle TSS data, but maybe one could point otherwise).
Many thanks in advance!