RNAFramework

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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/issues to: https://github.com/dincarnato/RNAFramework/issues

Author

Danny Incarnato (dincarnato[at]rnaframework.com)
University of Groningen

References

Incarnato et al., 2018. RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications. Nucleic Acids Research [PMID: 29893890]

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.

Documentation

For any information, please refer to the documentation: http://rnaframework-docs.readthedocs.io/