Circular RNA identification software tools | RNA sequencing data analysis
Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function.
Discovers splice junctions using approximate sequence similarity that is not dependent on features or locations of the splice sites. MapSplice is based on efficient approximate sequence alignment methods combined with a local search. It integrates a rigorous approach to increase specificity of the splice search. This tool is able to detect the exon splice junctions contained in the sampled mRNA transcriptome.
Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced suffix arrays (ESA): it aims to find the best-scoring seed for each suffix of a read. The tool lack, which rescues unmapped RNAseq, reads and works in conjunction with segemehl and many other frequently used split-read aligners, is distributed together with it.
Identifies circular RNAs (circRNAs) using multiple seed matching. CIRI is designed to differentiate back-spliced junction (BSJ) reads from non-BSJ reads using efficient maximum likelihood estimation (MLE) based on multiple seed matching. The software is optimized for the key steps in circRNA detection, including inferring original region for sequencing read segments and distinguishing BSJ reads from forward-spliced junction (FSJ) reads. The software is applicable to sequencing data with mixed read lengths, and can be run with multiple threads.
Detects head-to-tail spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) in RNA-seq data. find_circ is a pipeline that can find circRNAs in any genomic region. It takes advantage of long (,100 nucleotides) reads, and predicts the acceptor and donor splice sites used to link the ends of the RNAs. This method provides evidence that circRNAs form an important class of post-transcriptional regulators.
A combined strategy to identify junction reads from back spliced exons and intron lariats. CIRCexplorer is now only a circular RNA annotating tool, and it parses fusion junction information from mapping results of other aligners. The result of circular RNA annotating is directly dependent on the mapping strategy of aligners. Different aligners may have different circular RNA annotations. CIRCexplorer is now only in charge of giving fusion junctions a correct gene annotation.
Finds circular RNAs (circRNAs) from RNA-seq data, based on STAR. circRNA_finder is used for the prediction of circRNA with very proximal splice sites (below 100 bp). This tool works de novo without knowledge of gene annotations and exon-intron structures.
A computational pipeline to detect circular RNA from RNA-Seq data, based on junction reads from back spliced exons. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The current version of the UROBORUS pipeline can only detect those circRNAs supported by exon–exon junctions, and may miss those circRNAs derived from an intron region or intergenic region.