Methods

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a ...

SeqGSEA is an open-source Bioconductor package, for the functional integration of differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an analysis pipeline which first computes differential splicing (DS) and differential expression (DE) scores, followed by integrating them into ...

Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Due to the rapid increase in throughputs and decrease in costs of next generation ...

In multicellular organisms, biological function emerges when heterogeneous cell types form complex organs. Nevertheless, dissection of tissues into mixtures of cellular subpopulations is currently challenging. Researchers at the Weizmann Institute, Israel introduce an automated massively parallel single-cell RNA sequencing (RNA-seq) ...

Next-generation sequencing (NGS) is becoming one of the most widely used technologies in the field of genomics. Library preparation is one of the most critical, hands-on, and time-consuming steps in the NGS workflow. Each library must be prepared in an ...

Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how ...

COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS ...

Numerous high-throughput sequencing studies focus on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization, or trans-splicing are often neglected. Researchers from the University Leipzig, Germany introduce a novel, unbiased algorithm to detect splice ...

The production of DNA libraries in sufficient quantity and quality is not only the actual sequencing of the essential step in order to achieve meaningful results in accordance with Next Generation Sequencing (NGS ) process . Automated methods must be ...

Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie ...