Tag Archives: quantification

RNA sequencing (RNA-seq) is an integral tool in immunogenomics, allowing for interrogation of the transcriptome of a tumor and its microenvironment. Analytical methods to deconstruct the genomics data can then be applied to infer gene expression...

Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative ...

Iowa State University researchers propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and...

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all ...

By Lior Pachter –  One of the maxims of computational biology is that “no two programs ever give the same result.” This is perhaps not so surprising; after all, most journals seek papers that report a significant improvement to an existing method. ...

RNA sequencing (RNA-seq) is a widely applied technology that for extractings gene and transcript expression from biological samples. Given numerous quantification pipelines for RNA-seq data, one fundamental challenge is to determine identify a pipeline that can produce the most accurate ...

The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. Researchers at the Novartis Institutes for Biomedical Research have developed an integrated alignment workflow and a simple counting-based approach to derive estimates for gene, exon and ...

Researchers from the University of California, Berkeley  and the University of Iceland have developed kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing ...

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be ...

With the rapid development of NGS technologies, RNA-seq has become the new standard for transcriptome analysis. Although the price per base has been substantially reduced, sample preparation, sequencing and data processing are major cost factors in high throughput screenings. QuantSeq ...