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

Oxford Nanopore Conference London-Calling

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

The Genotype-Tissue Expression project (GTEx)

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

Kallisto, Kallisto, a new ultrafast 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

Genomic Imprinting in Reciprocal F1 Mice

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, […]

Inferring Cellular Localization from Single Cell RNA-seq

Thanks to RNA-seq, we have ways to estimate expression abundances decently (at least at gene level :-)).  One of the other missing dimensions in realm of  expression is where is that transcript expressed from? what is the physical location of the transcript?. Till recently, our ability to answer the positional information about the expressing transcript […]