PT - JOURNAL ARTICLE AU - Bo Li AU - Akshay Tambe AU - Sharon Aviran AU - Lior Pachter TI - Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays AID - 10.1101/063107 DP - 2016 Jan 01 TA - bioRxiv PG - 063107 4099 - http://biorxiv.org/content/early/2016/07/10/063107.short 4100 - http://biorxiv.org/content/early/2016/07/10/063107.full AB - A number of high-throughput transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and post-transcriptional modifications. Although these assays survey a diverse set of ‘epitranscriptomic’ marks, they share methodological similarities and as such their interpretation is predicated on addressing similar computational challenges. Among these, a key question is how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. In this paper, we propose PROBer, the first rigorous statistical model to handle these challenges for a general set of sequencing-based ‘toeprinting’ assays.