M2seq

M2seq is a set of Python and MATLAB scripts that extract mutate-and-map signals from Illumina next-generation sequencing data.

Features include:

• Separation of barcoded samples
• Alignment to reference sequences, and extraction of mutations
• Visualization of mutate-and-map signals in the resulting data
• Creation of RDATs that can be analyzed by tools in Biers.

Usage

• Getting started describes installations & BowTie2, SHAPEmapper, and other dependencies.
• Instructions and example data are available at README.md
• Analyze the output M2seq data with special instructions described in Biers.

License

Copyright © & BSD-3 license of M2seq Source Code is described in LICENSE.md.

Reference

Cheng, C. Kladwang, W. Yesselman, J. Das, R. (2017)
RNA structure inference through chemical mapping after accidental or intentional mutations
BioRxiv. | Paper | Link

Related Packages

• RDATKit
• Biers

Workflows

• I have just discovered an RNA molecule
• I want to learn an RNA’s secondary structure

Developed by Das lab, Leland Stanford Junior University.

README by Rhiju Das, August 2017.