kallisto paper summary: Near-optimal RNA-seq quantification

In case you missed it, kallisto, the new RNA-seq quantification method from Lior Pachter‘s group, was one of the biggest highlights from this year’s The Biology of the Genomes conference. kallisto team made the kallisto software immediately available and the preprint describing kallisto was available at arXiv pretty soon after the #BOG15. Near-optimal RNA-Seq quantification, Nicolas Bray, […]

Oxford Nanopore CTO Clive Brown’s Talk at London Calling: MinION ASIC, volTRAX, promethION

Oxford Nanopore is organising its first conference, a two day event) on all things nanopore in London, aptly named as London Calling. Among the many interesting talks , the most anticipated talks is from Oxford Nanopore CTO Clive Brown’s talk announcing the future things to expect from Oxford Nanopore. The talk did not seem to […]

Interesting papers from the GTEx (Genotype-Tissue Expression) Project

It has been a good week for RNA-seq enthusiasts. First, Kallisto, a new way to quantify transcript expression, happened at BOG15. And this weeks’ Science magazine has three interesting papers on the GTEx (Genotype-Tissue Expression) Project, dealing with boatload of RNA-seq data, a whopping 1641 human RNA-seq samples to be precise. In  addition, there are three […]

Kallisto, a new ultra fast RNA-seq quantitation method

[Update:] Since the post was published, a preprint on Kallisto manuscript is available. Lior Pachter has writtena blog post on pseudo-aligments and Rob Patro has a nice post on “Light weight algorithms for RNA-seq”. Here there. kallisto preprint Near-optimal RNA-Seq quantification with kallisto Rob Patro’s blog post: Not-quite alignments: Salmon, kallisto and efficient quantification of […]

An Atlas of Genomic Imprinting in Mouse and Human Using RNA-seq data

Nature Genetics has a new paper cataloging genomic imprinting in mouse (and human) across multiple tissues. Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse, Tomas Babak, Brian DeVeale, Emily K Tsang, Yiqi Zhou, Xin Li, Kevin S Smith, Kim R Kukurba, Rui Zhang, Jin Billy Li, Derek van der Kooy, […]