Fig. 1

Workflow of APA-Scan. Starting with aligned RNA-seq and 3′-end-seq (optional) bam files, APA-Scan consists of three steps and generates high quality graphical illustration of aligned sequences with the indication of 3′-UTR APA events. A Read coverage files are generated for RNA-seq and 3′-end-seq (if provided) input samples. B APA-Scan identifies potential cleavage sites according to polyadenylation signal (PAS) hexamer: ATTAAA or AATAAA, or 3′-end peaks (if 3′-end-seq data is available). C Graphical illustration of the identified events. The illustration also highlights unannotated short 3′-UTR transcript identified from this task. The vertical red lines show the corresponding cleavage sites