PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.

ABSTRACT: A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. We introduce PROBer, a statistical model and associated software, that addresses this challenge for the analysis of toeprinting assays. PROBer takes sequencing data as input and outputs estimated transcript abundances and isoform-specific modification profiles. Result

SUBMITTER: Li B 

PROVIDER: S-EPMC5758053 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature