As a revolutionary technology for life sciences, RNA-seq has many applications and the computation pipeline has also many variations. Researchers from the Functional Genomics Center Zurich describe a protocol to perform RNA-seq data analysis where the aim is to identify differentially ...
Read More »You’ve been aligning your RNA-Seq reads all wrong
Sequence read alignment to a reference genome is a fundamental step in many genomics studies. Accuracy in this fundamental step is crucial for correct interpretation of biological data. In cases where two or more closely related bacterial strains are being ...
Read More »The PARA-suite – PAR-CLIP specific sequence read simulation and processing
Next-generation sequencing technologies have profoundly impacted biology over recent years. Experimental protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), which identifies protein-RNA interactions on a genome-wide scale, commonly employ deep sequencing. With PAR-CLIP, the incorporation of photoactivatable nucleosides into ...
Read More »RapMap – a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
The alignment of sequencing reads to a transcriptome is a common and important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a transcriptome (as is common in the de novo setting or when a trusted reference ...
Read More »A survey of best practices for RNA-seq data analysis
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. A multi-national team led by researchers from the University of Florida reviews all of the major steps in RNA-seq data analysis, including ...
Read More »RNASequel – accurate and repeat tolerant realignment of RNA-seq reads
RNA-seq is a key technology for understanding the biology of the cell because of its ability to profile transcriptional and post-transcriptional regulation at single nucleotide resolutions. Compared to DNA sequencing alignment algorithms, RNA-seq alignment algorithms have a diminished ability to ...
Read More »miRseqViewer – Multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data
Deep sequencing of small RNAs has become a routine process in recent years, but no dedicated viewer is as yet available to explore the sequence features simultaneously along with secondary structure and gene expression of microRNA (miRNA). A team led ...
Read More »Visualization of nucleotide substitutions in the (micro)transcriptome
RNA-related applications of the next-generation sequencing (NGS) technologies require context-specific interpretations: e.g., sequence mismatches may indicate sites of RNA editing, or uneven read coverage often points to mature form of microRNA. Existing visualization tools traditionally show RNA molecules in two ...
Read More »FANSe2: A Robust Tool for Quantitative NGS Applications
Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) ...
Read More »BBMap (aligner for DNA/RNA-Seq) is now open-source and available for download
BBMap is now available here: https://sourceforge.net/projects/bbmap/ BBMap/BBtools are now open source. Please try it out – it’s a 3MB download, and written in pure Java, so installation is trivial – just unzip and run. Handles all platforms (Illumina, PacBio, 454, ...
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