Tag Archives: kallisto

RNA-Seq data analysis has become vital to understanding gene structure and expression patterns in transcriptomic studies. A typical reference genome guided RNA-Seq workflow...

The Chan Zuckerberg Initiative (CZI) announced $3.8 million in funding for 23 grants to support open source software projects essential to biomedical research, enabling software maintenance, growth, development, and community engagement. As part of CZI’s Essential Open Source Software for ...

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  Researchers from the Keck School of Medicine of USC offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates ...

Alternatively spliced transcript isoforms are commonly observed in higher eukaryotes. The expression levels of these isoforms are key for understanding normal functions in healthy tissues and the progression of disease states. However, accurate quantification of expression at the transcript level ...

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. ...

The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in ...

Caltech researchers describe sleuth, a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that ...

RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at ...

A brief introduction to the theory and method underlying kallisto for transcript quantification of RNA-Seq data. This screencast is from our IIHG MiniCourse training series on bioinformatic methods for U Iowa researchers. Find IIHG on the web at: http://www.medicine.uiowa.edu/humangenetics/

Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is typically not easily usable ...