Software for analysis of NGS chemical mapping experiments
MAPseeker is a software package for analyzing chemical mapping data from next-gen sequencing experiments, such as Multiple Adduct Probing read out through deep Sequencing (MAP-seq) and Multiplexed •OH Cleavage Analysis read out through deep Sequencing (MOHCA-seq). It includes an executable for performing sequence alignment and reverse transcription stop counting, as well as MATLAB scripts for calculating chemical reactivities and outputting data to RDAT text format and Python scripts for optional pre-processing of RNA fasta files.
MAPseeker can be downloaded for non-commercial use at the RMDB. Commercial users, please contact us.
Installation instructions and tutorials for analyzing MAP-seq and MOHCA-seq data are provided in the README.md file in the package. The package also includes example MAP-seq and MOHCA-seq data.
Copyright © of MAPseeker Source Code is described in LICENSE.md.
Seetin, M. G., Kladwang, W., Bida, J. P. & Das, R. (2014)
Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol
Methods in Molecular Biology 1086: 95 - 117. | Paper | Link
Cheng, C. Y., Chou, F.-C., Kladwang, W., Tian, S., Cordero, P. & Das, R. (2015)
Consistent global structures of complex RNA states through multidimensional chemical mapping
eLife 4: e07600. | Paper | Link
Developed by Das lab, Leland Stanford Junior University.
README by Clarence Cheng, May 2016.
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