Are our reviewers correct or incorrect?
About two months ago we got back reviews for our assembly artifacts paper, in which we showed that there was a strong 3' bias in the reads towards higher graph connectivity. Since shotgun sequencing is supposed to be random, we asserted that this 3' …
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A week or two ago, I posted a crazy idea about crowdsourcing a bioinformatics analysis pipeline. I may still try to do that. But in the meantime, here's another crazy idea.
First, some background.
I'm writing this as I fly back from …
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I'm worried about our current mRNAseq analysis strategies.
I recently posted a draft paper of ours to arXiv entitled RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates; the link is to the Haldane's Sieve discussion of the paper. Graham Coop said I should write something quick, and so …
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Over the last few weeks, I've been on a bit of a Cory Doctorow kick. I started by reading Homeland, a sequel to the excellent Little Brother; these two very important books about anti-terror-enabled government suppression of liberty and free speech are very well written and extremely timely. I then …
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Or, "can we crowdsource BGI?" ;)
With all of the crazy need surrounding genomic analysis -- most of it on a shoestring budget -- I am thinking about a mildly crazy idea.
What if I offered to computationally analyze people's non-model transcriptomic and metagenomic data for them, in exchange for (a) non-exclusive access …
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I just finished attending a 1-day workshop on Cyberinfrastructure for Marine 'Omics down in DC. It was a meeting organized by the Gordon and Betty Moore Foundation but attended by program managers from about a dozen different agencies and divisions (NSF BIO, NSF GEO, etc.); a bunch of pretty serious …
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I'm on my way down to D.C. to attend another meeting about cyberinfrastructure, this time with a bent towards metagenomics pipelines. (At least, I'm pretty sure that's why I'm invited. It's getting hard to tell these days.)
Inspired by James Watters' blog post on his "fork you" shirt, I …
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