| 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. |
|
Site Map
Releases
| 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
Installation (v1.0.1 and earlier)Spats runs on intel-based computers running Linux or Mac OS X and that have GCC 4.0 or greater installed. Currently spats must be built from the source code, though we recognize the need for an easier installation system. Several pieces of software are required to run the spats pipeline. The software below should be installed in the order listed. Detailed instructions are given for a Path SetupThe creation of a local installation of spats is recommended. Currently we recommend creating the following directory structure: <path_prefix>/SHAPE-Seq/which should contain: <path_prefix>/SHAPE-Seq/bin/ <path_prefix>/SHAPE-Seq/bin/bin/ <path_prefix>/SHAPE-Seq/bin/lib/ <path_prefix>/SHAPE-Seq/src/ <path_prefix>/SHAPE-Seq/build/Here <path_prefix> is the location of this directory on your system. To ensure that these paths will be used correctly by the installation system, it is helpful to add them to your default shell, for example in bash by including the following lines in your .bash_profile: export PATH=$PATH:<path_prefix>/SHAPE-Seq/bin:<path_prefix>/SHAPE-Seq/bin/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_prefix>/SHAPE-Seq/bin/lib export PYTHONPATH=$PYTHONPATH:<path_prefix>/SHAPE-Seq/bin/bin Installing FastX_Spats_Toolkit and LibGTextUtils (Required)fastx_spats_toolkit and libgtextutils are required for adapter trimming. Instructions for installing via sourcecode:
Installing Bowtie (Required)bowtie is used to align next-generation sequencing reads. Bowtie version 0.12.8 is required. Spats is not currently compatible with Bowtie 2.
Installing Boost (Required)boost version 1.49.0 is required.
If you are on a 32-bit Linux system, type (all on
one line): bjam --prefix=<path_prefix>/SHAPE-Seq/bin/ --toolset=gcc --architecture=x86 --address_model=32 --link=static --runtime-link=static --stage=install If you are on a 64-bit Linux system, type (all on
one line): bjam --prefix=<path_prefix>/SHAPE-Seq/bin/ --toolset=gcc --architecture=x86 --address_model=64 --link=static --runtime-link=static --stage=install Installing Cutadapt (Required)We currently use cutadapt version 1.5
Building Spats (Required)We currently recommend installing spats version 1.0.0.
|