DNASTAR announced the release of Lasergene 13 today, which significantly advances scientists’ ability to perform RNA research on model and non-model organisms on standard desktop computers. Significant software enhancements include the ability to perform de novo transcriptome assembly of RNA ...
Read More »BinPacker – Packing-Based De Novo Transcriptome Assembly from RNA-Seq Data
High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. Now, ...
Read More »Analysis of RNA-Seq Data Using TopHat and Cufflinks
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge amounts of data in a very short span of time for a single sample. These data have required the parallel advancement of computing tools to organize and interpret ...
Read More »SATRAP – SOLiD Assembler TRAnslation Program
SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space sequences. ...
Read More »Optimization of next generation sequencing transcriptome annotation for species lacking sequenced genomes
Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods ...
Read More »Current limitations of RNA-seq analysis for detection of novel transcripts
Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques ‘RNA sequencing (RNA-seq)’ is rapidly replacing microarray-based techniques in laboratories ...
Read More »A comparative study of RNA-seq analysis strategies
Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a ...
Read More »StringTie – improved reconstruction of a transcriptome from RNA-Seq reads
Methods used to sequence the transcriptome often produce more than 200 million short sequences. Researchers at Johns Hopkins University have developed StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de ...
Read More »ISP – Accurate inference of isoforms from multiple sample RNA-Seq data
RNA-Seq based transcriptome assembly has become a fundamental technique for studying expressed mRNAs (i.e ., transcripts or isoforms) in a cell using high-throughput sequencing technologies, and is serving as a basis to analyze the structural and quantitative differences of expressed ...
Read More »RNA Bioinformatics – New RNA-Seq Protocols from Methods in Molecular Biology
RNA Bioinformatics Edited by Ernesto Picardi ISBN: 978-1-4939-2290-1 (Print) 978-1-4939-2291-8 (Online) Analysis of High-Throughput RNA Sequencing Data Quality Control of RNA-Seq Experiments Xing Li, Asha Nair, Shengqin Wang, Liguo Wang Pages 137-146 Accurate Mapping of RNA-Seq Data Kin Fai Au ...
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