Updating exon junctions, TSSs, and CPSs in transfrag models. (A) Shown is a workflow for updating transfrag models, which comprises two steps: (1) updating exon junctions, and (2) updating TSSs and CPSs. (B) The number of neighboring transfrag pairs supported by putative splicing signals (red), by exon-junction reads (navy), and by neither (olive) in HeLa cells. The numbers in parentheses in the key indicate the number of pairs in each group. Among exon junctions supported by either exon-junction reads or putative splicing signals, the fractions of known (cyan) and novel (gray) exon junctions in GENCODE annotations are shown in the inset. (C) The fraction of transfrags updated with both TSS and CPS (blue), with only TSS (yellow), with only CPS (magenta), and with neither TSS or CPS (gray) in HeLa cells. (D) The number of TFBSs upstream of the original 5′ end (blue) and of the 5′ end updated with a TSS (pink) in HeLa cells. (E) The number of transfrags with a close poly(A) signal, AAUAAA, over the relative distances from the original 3′ end (blue) and the 3′ end updated with a CPS (pink) of transfrags in HeLa cells.
