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Important

[06-12-2018] RNA Framework v2.6.1 [minor release]:
- Added mutated reads statistics to rf-count
- Fixed 2 bugs in rf-fold, one causing folding to fail with pseudoknotted structures in windowed mode, the other causing the software to crash when windowed analysis was performed using window sizes < 50 nt
- Modified rf-count to handle reference sequences with degenerated bases

Introduction

The recent advent of Next Generation Sequencing (NGS) techniques, has enabled transcriptome-scale analysis of the RNA epistructurome. Despite the establishment of several methods for querying RNA secondary structures (CIRS-seq, SHAPE-seq, Structure-seq, DMS-seq, PARS, SHAPE-MaP, DMS-MaPseq), and RNA post-transcriptional modifications (Ψ, m1A, m6A, m5C, hm5C, 2'-OMe) on a transcriptome-wide scale, no tool has been developed to date to enable the rapid analysis and interpretation of this data.

RNA Framework is a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data.
Its main features are:

  • Automatic reference transcriptome creation
  • Automatic reads preprocessing (adapter clipping and trimming) and mapping
  • Scoring and data normalization
  • Accurate RNA folding prediction by incorporating structural probing data

For updates, please visit: http://www.rnaframework.com
For support requests, please post your questions to: https://groups.google.com/forum/#!forum/rnaframework

Author

Danny Incarnato (dincarnato[at]rnaframework.com)
Epigenetics Unit @ HuGeF [Human Genetics Foundation]

Reference

Incarnato et al., (2018) RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications (Nucleic Acids Research, in press).

Incarnato et al., (2015) RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data (PMID: 26487736).

License

This program is free software, and can be redistribute and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.

Please see http://www.gnu.org/licenses/ for more information.

Prerequisites

Installation

Clone the RNA Framework git repository:

git clone https://github.com/dincarnato/RNAFramework

This will create a "RNAFramework" folder.
To add RNA Framework executables to your PATH, simply type:

export PATH=$PATH:/path/to/RNAFramework