[07-01-2018] RNA Framework v2.5.1 [major release]:
- New tool RF JackKnife introduced to perform jackknifing (grid search) of optimal slope/intercept folding parameters
- Changed the RC format's standard (from now on RNA Framework will support backward compatibility for obsolete RC files, however RC files generated using previous versions of the RNA Framework are no longer supported)
- Introduced RF Fold support for windowed folding and pseudoknots prediction (entire API rewrite to support pseudoknotted base-pairs)
- RF PeakCall now supports the analysis of immunoprecipitation experiments lacking a control/input sample
- RF Norm support for Siegfried et al., 2014 data normalization method added back (now supports also the analysis of experiments lacking a denatured control sample)
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
Danny Incarnato (dincarnato[at]rnaframework.com)
Epigenetics Unit @ HuGeF [Human Genetics Foundation]
Incarnato et al., (2015) RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data (PMID: 26487736).
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.
- Linux/Mac system
- Bowtie v1.1.2 (http://bowtie-bio.sourceforge.net/index.shtml), or
Bowtie v2.2.7 or greater (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
- SAMTools v1.2 or greater (http://www.htslib.org/)
- BEDTools v2.0 or greater (https://github.com/arq5x/bedtools2/)
- Cutadapt v1.10 or greater (http://cutadapt.readthedocs.io/en/stable/index.html)
- ViennaRNA Package v2.2.0 or greater (http://www.tbi.univie.ac.at/RNA/)
- RNAstructure v5.6 or greater (http://rna.urmc.rochester.edu/RNAstructure.html)
- Perl v5.12 (or greater), with ithreads support
Perl non-CORE modules (http://search.cpan.org/):
- RNA (installed by the ViennaRNA package)
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: