Progress and challenges in profiling protein–RNA and protein-associated RNA–RNA interactions

Workflow of computational pipeline in CLIP and chimeric CLIP protocols. (Left) Analysis for CLIP and chimeric CLIP involves standard adaptor trimming, genomic mapping, and peak calling. (Right) Specific modifications for chimeric CLIP include (top) premasking of nonchimeric reads, (middle) an initial mapping pass to identify candidate chimeric reads, and (bottom) single or sequential mapping steps to map the remaining chimeric target fragment with high specificity.