spats

About Spats

Spats is a package originally developed to support:

Julius B. Lucks, Stefanie A. Mortimer, Cole Trapnell, Shujun Luo, Sharon Aviron, Gary P. Schroth, Lior Pachter, Jennifer A. Doudna, and Adam P. Arkin, SHAPE-Seq: Multiplexed RNA Secondary and Tertiary Structure Determination PNAS, 2011, doi: 10.1073/pnas.1106501108
Sharon Aviran, Cole Trapnell, Julius B. Lucks, Stefanie A. Mortimer, Shujun Luo, Gary P. Schroth, Jennifer A. Doudna, Adam P. Arkin, and Lior Pachter, Modeling and automation of SHAPE-Seq analysis PNAS, 2011, doi: 10.1073/pnas.1106541108

and now supports:

David Loughrey, Kyle E. Watters, Alexander H. Settle, and Julius B. Lucks SHAPE-Seq 2.0: Systematic Optimization and Extension of High-Throughput Chemical Probing of RNA Structure with Next Generation Sequencing Nucleic Acids Research, 2014 .
Kyle E. Watters, Timothy R. Abbott, and Julius B. Lucks Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq Nucleic Acids Research, 2015
Kyle E. Watters, Angela M Yu, Eric J. Strobel, Alexander H. Settle, and Julius B. Lucks Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) Methods, 2016
Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB. Cotranscriptional folding of a riboswitch at nucleotide resolution Nature Structure and Molecular Biology 10.1038/nsmb.3316
Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB. Cotranscriptional folding of a riboswitch at nucleotide resolution Nature Structure and Molecular Biology 10.1038/nsmb.3316

and other papers from the SHAPE-Seq community.

The Spats package implements a read mapping and reactivity analysis pipeline for calculating SHAPE-Seq reactivities from an input set of next-generation reads. The reactivity calculation implemented is described in:

Sharon Aviran, Julius B. Lucks, and Lior Pachter RNA Structure characterization from chemical mapping experiments. 49th Allerton Conference, UIUC 2011. doi: 10.1109/Allerton.2011.6120379 .

For more information about the SHAPE-Seq experiment, and the application of spats for data analysis, please see:

Stephanie A. Mortimer, Cole Trapnell, Sharon Aviran, Lior Pachter, and Julius B. Lucks SHAPE-Seq: High Throughput RNA Structure Analysis Current Protocols in Chemical Biology, 2012, doi: 10.1002/9780470559277.ch120019