Tag Archives: variant

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized ...

Researchers at the Broad Institute have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. This method uses targeted RNase H-based digestion ...

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. Researchers at the European Molecular Biology Laboratory present HTSeq, a ...

RNA sequencing (RNA-seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole-genome single nucleotide polymorphism (SNP) variant information, the allele frequency can ...

RNA-Seq has become the method of choice to quantify genes and exons, discover novel transcripts, and detect fusion genes. However, reliable variant identification from RNA-Seq data remains challenging due to the complexities of the transcriptome, the challenges of accurately mapping ...

Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here a team ...

High-throughput sequencing of RNA in vivo facilitates many applications, not the least of which is the cataloging of variant splice isoforms of protein-coding messenger RNAs. While many solutions have been proposed for reconstructing putative isoforms from deep sequencing data, these ...