| Spats processes reads and calculates SHAPE reactivities for SHAPE-Seq
experiments on multiple RNAs. It accepts raw paired-end sequencing reads in FASTQ format, and a target
sequence file containing the sequences of RNAs present in the experimental pool. Spats then performs
read alignment to calculate distributions of read ends in the SHAPE (+) and (-) channel for each
nucleotide in each RNA. Spats then estimates nucleotide resolution SHAPE reactivities for each RNA,
using a model-driven maximum likelihood procedure based on a model of the reverse transcriptase
process used in the SHAPE-Seq experiment.
Spats is a collaborative effort between the
Aviran Lab at UC Davis, the Pachter Lab at UC Berkeley, the
Trapnell Lab
at the University of Washington, and
the Lucks Lab
at Northwestern University. Spats is provided under the OSI-approved Boost License. fastx_spats_toolkit_v_0.1.0 is provided under the AGPLv3 License. |
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Site Map
Releases
| spats version 1.0.2 | 5/30/2017 |
| Source code | |
| spats version 1.0.1 | 9/10/2016 |
| Source code | |
| spats version 1.0.0 | 3/21/2016 |
| Source code | |
| spats version 0.8.0 | 9/4/2014 |
| Source code | |
| fastx_spats_toolkit version 0.1.0 | 9/4/2014 |
| Source code | fastx_spats_toolkit version 0.1.0 - binary distribution for 64-bit GNU/Linux 2.6.18 | 9/4/2014 |
| Source code | |
| spats version 0.7.0 | 4/10/2012 |
| Source code |
Publications
Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure
PNAS 10.1073/pnas.1106541108Aviran S, Lucks JB, Pachter L. RNA structure characterization from chemical mapping experiments
Proceedings of the 49th Allerton Conference on Communication, Control, and Computing, 1743-1750, 2011Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
PNAS 10.1073/pnas.1106501108
Mortimer SA, Trapnell C, Aviran S, Pachter L and Lucks JB. SHAPE-Seq High Throughput RNA Structure Analysis
Current Protocols in Chemical Biology10.1002/9780470559277.ch120019
Loughrey D, Watters KE, Settle AH, and Lucks JB. SHAPE-Seq 2.0: Systematic Optimization and Extension of High-Throughput Chemical Probing of RNA Structure with Next Generation Sequencing
Nucleic Acids Research 10.1093/nar/gku909
Aviran S and Pachter L. Rational experiment design for sequencing-based RNA structure mapping
RNA 10.1261/rna.043844.113
Watters KE, Abbott TR, and Lucks JB. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq
Nucleic Acids Research 10.1093/nar/gkv879
Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB. Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
Methods 10.1016/j.ymeth.2016.04.002
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
Other Contributors
- Stefanie Mortimer
- Shujun Luo
- Gary Schroth
- Adam Arkin
- Jennifer Doudna
Links
InstallationSpats runs on intel-based computers running Linux or Mac OS X. Currently spats can be run from the released binaries and can be built from the source code.
Click here for installation instructions for earlier versions of spats. |