[2022-05-31] RNA Framework v2.8.0 [major release]:
Introduced two new modules.
rf-count-genome to handle genome-level SAM/BAM alignments.
rf-structextract to extract structure motifs according to user-defined criteria (including elements residing within low reactivity - low Shannon entropy regions). Introduced
rf-rctools extract tool to allow extracting regions of interest from an RC file, provided a BED or GTF annotation. Please check the changelog for a complete list of the changes
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
Danny Incarnato (dincarnato[at]rnaframework.com)
University of Groningen
Incarnato et al., (2018) RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications (PMID: 29893890).
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 v1.2.3 (http://bowtie-bio.sourceforge.net/index.shtml), or
Bowtie v2.3.5 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 v2.1 or greater (http://cutadapt.readthedocs.io/en/stable/index.html)
- ViennaRNA Package v2.4.0 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: