RT Journal Article
SR Electronic
T1 Prober: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 063107
DO 10.1101/063107
A1 Bo Li
A1 Akshay Tambe
A1 Sharon Aviran
A1 Lior Pachter
YR 2016
UL http://biorxiv.org/content/early/2016/07/12/063107.abstract
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.