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We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

The GTEx methods debate

Kate Blair

Featured, The Future of Work

This week, a dialogue erupted around the Genotype-Tissue Expression (GTEx) Consortium and its methods for analyzing RNA-Seq data. Tracking the debate will take you through Twitter threads, into blog posts, down comments sections, past PubMed entries, and over Nature‘s login wall.

A mystery muscle lincRNA

Nate

Science

We know that our whole genome is distributed to (almost) every cell of our bodies. This fact can be used both to surprise introductory biology students and to usefully refine a fundamental scientific question. Instead of merely asking how it comes to be that different parts of our bodies have

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RNA-Seq Interactive Literature Review

Kate Blair

Featured, Science

RNA-Seq is fast becoming the top method for examining the transcriptional activity of genomes. In the five years since the first publications described the technology, RNA-Seq has enabled the discovery of new transcripts in well-studied genomes, challenged our views of imprinting, offered insights into the biology of cancer, and transformed new

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Short read alignment: seeding

Nate

Science

In my last post I explained some of the basics of short read alignment algorithms. Go read it if you like; if not, recall that: Many modern alignment algorithms rely on what is called seeding and extending. “Seeding” is finding exact matches of part of the read with part of the

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Short read alignment: an introduction

Nate

Science

Biologists today often find themselves with lots of–say, 10^6–short sequences of DNA from a sample, and their ability to do scientifically useful things with those sequences depends on their ability to align those sequences to a reference sequence. Many of the hard and important projects in genomics either are alignment

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Unicorn genome sequence announced

brandi

Featured, Science

A landmark genome announcement was made by the Equid Sequencing Consortium today. Scientists hope that the new data will explain origins of the horn and help identify key genes that drive horn development. A high-quality draft of unicorn genome was published today and will be submitted to GenBank later this spring.

Visualizing exome coverage depth

Nate

Product News

The coverage of a base pair in a sequencing run is the number of times that it was sequenced. We usually estimate coverage in an intuitive way: by comparing the total amount of measurement to the total amount of stuff to be measured. Dividing the total length of the reads

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