Methods

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

rna-seq

Given increasing numbers of RNA-seq samples in the public domain, researchers at the University of Groningen studied to what extent expression quantitative trait loci (eQTLs) and allele-specific expression (ASE) can be identified in public RNA-seq data while also deriving the ...

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Researchers Develop Tool to Better Visualize, Analyze Human Genomic & Transcriptomic Data

rna-seq

Scientists at the University of Maryland have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. The free tool, called Epiviz, was described in ...

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A comparison of De novo short read sequence assemblers

rna-seq

The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, ...

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bagSVM – Classification of RNA-Seq Data via Bagging Support Vector Machines

RNA sequencing (RNA-Seq) is a powerful technique for transcriptome profiling of the organisms that uses the capabilities of next-generation sequencing (NGS) technologies. Recent advances in NGS let to measure the expression levels of tens to thousands of transcripts simultaneously. Using ...

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JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

rna-seq

JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of ...

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An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

rna-seq

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in ...

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iRegulon: From a Gene List to a Gene Regulatory Network

rna-seq

Identifying master regulators of biological processes and mapping their downstream gene networks are key challenges in systems biology. Researchers at the KU Leuven Center for Human Genetics developed a computational method, called iRegulon, to reverse-engineer the transcriptional regulatory network underlying ...

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