Exploration of TSR presupposes that you have TSR to explore. There are different experimental techniques for 5'-end transcript profiling. Our computational analyses should be applicable to sequencing data from any such techniques (both single- and paired-end read data). The workflow involves the following basic steps:
- mapping of the read data to the relevant genome
- identifying TSS and TSR
- exploring the TSR
- (possibly) identification of transcription regulatory motifs
The following github repositories provide tools and documentation for all of the steps (in order):
- GoSTRIPES
- TSRchitect (also available as a Bioconductor package)
- TSRbuild (this repository)
- MoVRs
Here we walk you through the data work described in our publications:
Policastro2020 Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel, and Gabriel E. Zentner (2019) Simple and efficient mapping of transcription start sites with STRIPE-seq. In review.
Ganote2020 Ganote, C. & Brendel, V.P (2020) Identification and characterization of plant promoters. The Plant Cell, to be submitted
TSRexploreR Robert A. Policastro et al. (2020) TSRexploreR: A tool set for evaluation and characterization of transcription start regions in eukaryotic genomes. In preparation.
Please see instructions on how to proceed in the named subdirectories.