TSRbuild: Scripts and workflows for building transcription start regions (TSR) from 5'-mRNA sequence data

The TSRbuild repository encompasses workflows and scripts developed in the Brendel and Zentner groups for analyses of transcription start sites (TSS) and regions (TSR) based on mRNA 5'-end short read sequencing data. The code conforms to our RAMOSE philosophy: it generates reproducible, accurate, and meaningful results; it is open (source) and designed to be scalable and easy to use.

The applications discussed here rely on code from our other repositories, in particular

• GoSTRIPES
• TSRchitect (also available as a Bioconductor package)

The main purpose of the exposition here is to provide examples of complete integration of different code components to entire reproducible workflows that encompass all analysis steps from read processing and alignment to determination and visualization of TSS and TSR.

Quick Start

Please go to the work directory and follow the instructions in the README file.

Reference

Robert A. Policastro, Daniel J. McDonald, Volker P. Brendel, and Gabriel E. Zentner (2020) GoSTRIPES and TSRexploreR: flexible workflows for processing, analysis, and visualization of STRIPE-seq data. In preparation.

Contact

Please direct all comments and suggestions to Volker Brendel at Indiana University.