Figure 9.

Strategies for extracting RNA structures and interactions from cross-link-ligation data. (a) Various types of cross-linked conformations by different chemical cross-linkers. (b) Classification and rearrangement of reads to 5 major categories, mapped to a reference genome (ref.). (c) Two basic types of binary constraints: basepaired duplex or contact/proximity. (d) Detection of high level structures by combining gap1 and gapm reads. (e) Detection of homodimers using reads with overlapped arms. (f) Clustering of gapped reads into duplex groups (DGs) using graph theory (network techniques). (g) Calculation of relative structure strength using the coverage fraction (covfrac) method. (h) Clustering and visualization of DGs into nonoverlapping groups (NGs).