Methods

Differential Poly(A) Tail Length Analysis Using Nanopore Sequencing

Summary This methods chapter describes a protocol for transcriptome-wide measurement of differential poly(A) tail lengths using nanopore direct RNA sequencing, combined with linear mixed models for statistical analysis. The approach enables quantitative comparison of poly(A) tail dynamics across conditions and provides a framework for studying the role of deadenylation in post-transcriptional gene regulation.

cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries

Summary This methods chapter describes cCLIP-seq, a computational approach for identifying and retrieving chimeric reads from HITS-CLIP libraries, where a small RNA and its target RNA are co-ligated and sequenced as a single molecule. By resolving these chimeric tags, cCLIP-seq enables direct identification of small RNA binding sites and precise base-pairing profiles at single-nucleotide resolution.