Intron retention identification software tools | RNA sequencing data analysis
Alternative splicing (AS) affects up to 95% of multi-exonic genes in humans. The three main types of AS are exon skipping, alternative 5′ or 3′ usage and intron retention (IR). IR occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. It constitutes a class of AS that is often neglected because these events are difficult to measure reliably.
Tests for differential usage of exons and hence of isoforms in RNA-seq samples. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation into account. It also detects with high sensitivity genes, and in many cases exons, that are subject to differential exon usage. DEXSeq achieves reliable control of false discovery rates by estimating variability for each exon or counting bin and good power by sharing dispersion estimation across features.
Offers a model for alternative splicing (AS) at exon or isoform level. MISO is a program that uses information in single-end or paired-end RNA-seq data and a Bayesian inference to estimate the probability for a read to be issued from a particular isoform. The program is available through two packages: in C language (fastmiso) or in Python language (misopy). The application supplies confidence intervals (CIs) for: (i) estimating of exon and isoform abundance, (ii) identifying differential expression. It can be applied for analyzing isoform regulation.
Assists in discovering alternative splicing (AS) events in transcripts predicted from RNA-seq data and in comparing them across multiple conditions. ASprofile is a program that can analyze all pairs of transcripts in the sixteen tissues to determine exons included in one transcript and skipped in the other. To realize these operations, this software is composed of several tools: “extract-as”; “extract-as-fpkm”; and “collect-fpkm”.
Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements. It is able to detect coding potential of transcripts, determines untranslated region (UTR) and open reading frame (ORF) lengths and predicts whether transcripts are nonsense mediated decay (NMD)-sensitive based on compatible annotated start codon positions and their downstream ORF.
Identifies correctly intron retention (IR) events and measured the ratio of retained introns to correctly spliced introns with great accuracy. IRFinder was developed to accurately detect IR from mRNA sequencing data. It implements an end-to-end analysis of retained introns from mRNA sequencing data in multiple species. It also includes alignment via the STAR algorithm, quality controls on the sample analyzed, IR detection, and quantification and statistics for comparing IR levels between multiple samples. IRFinder is a part of bioinformatics tools developed by CNRS to study the impact of intron retention on gene regulation.
Serves for the detection of genome-wide. iREAD works with both single-end and paired-end sequencing data that has been prepared using poly-A enrichment. The resulting intron retention contents can be explored in various ways such as functional enrichment and differential expression. It represents a generic tool to interrogate the previously largely neglected intronic regions from the angle of view of intron retention.
Investigates splice junctions and alternative splicing (AS) events from RNA-Seq data. SplicingViewer provides a platform dedicated to the visualization of AS patterns. The software first aligns short reads to reference genome, then detect of candidate splice junctions, and, lastly align unmapped short reads to splice junctions. It also displays genome mapping and junction mapping reads.