Spats

Read Processing and Reactivity Generation for SHAPE-Seq

   
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.
Open Source
	                    Software

Site Map

Releases

Publications

Other Contributors

Links

Installation


Spats 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.