For anyone who actually wants to know what it is I do, I've updated my lab Web site, http://ged.msu.edu/, to be a bit more representative of what it is we're doing these days. (I wrote it over three years ago, so it's been becoming increasingly dated.) In …
read moreThere are comments.
I just flew back from Montreal, where I gave a talk at the International Tunicate Meeting on the Molgula project. This is a project wherein we are doing quantitative mRNA sequencing on two species of ascidians, or sea squirts -- specifically, on M. oculata (tailed), M. occulta (tailless) -- and their hybrids …
read moreThere are comments.
First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:
fasta_file soil-data.fa qc_filter min_length=50 remove_Ns=true graph_filter min_length=400 velvet_assemble k=33 min_length=1000 scaffolding=True
Then I specify machine parameters, e.g. 'bigmem.conf':
[defaults] n_threads …read more
There are comments.
If you've been under a rock (or indulging in arsenic yourself), you've heard about NASA's "arsenic" article, claiming the discovery of a microbial species that can substitute arsenate for phosphate. The paper was pre-announced via a press conference that then announced the results.
Immediate blogtastrophe! The paper was critically reviewed …
read moreThere are comments.
In thinking about open science and open communication about science, I've always been frustrated by the people who claim that the risks outweight the benefit. Their arguments seem sound if you buy into a certain kind of logic (the creationists will try to twist whatever you say! the climate change …
read moreThere are comments.
(with Billie Swalla)
I've spent the last two weeks out at the Roscoff Statione Biologique in Roscoff, France. This little port is on the northern coast of the French region of Bretagne, or Brittany. I'm here with Billie Swalla, a professor at UW Seattle, and Elijah Lowe, a Computer Science …
read moreThere are comments.
(with Adina Howe, Jason Pell, Rosangela Canino-Koning, and Arend Hintze).
A few weeks ago I blogged a bit about a k-mer filtering system, khmer, that we were using to reduce metagenomic data to a more tractable size by throwing out error-prone reads (see A memory efficient way to remote …
There are comments.