[01-18-2017] rf-count v2.0.2b released (Major bug fixes):
1. In mutation count mode, deletions were shifted downstream by 1 nt
2. When calculating reference coverage, additional coverage was erroneously added to the base following read's end mapping position
3. In mutation count and coverage only modes, reads mapping to the reverse strand were erroneously discarded
4. In mutation count mode, when filtering mutations by minimum quality, the wrong read position was considered
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: