Author Archives: Nicholas Crawford

About Nicholas Crawford

I'm a computational genomics Post Doctoral Fellow at the California Academy of Sciences. I'm working on a number of projects including vertebrate systematics and the genomics of adaptation in lizards, heliconius butterflies, and Hawaiian drosophila.

Getting started with Ultra Conserved Elements

Cross posted on ngcrawford.com If you attended Evolution 2013, you probably heard quite a lot of chatter about ultra conserved elements. Essentially, ultra conserved elements (UCEs) are parts of the genome that are highly conserved between different species. Although UCEs … Continue reading

Posted in genomics, methods, phylogenetics | 1 Comment

A Tweak to Illumina Library Prep

For those readers who are making Illumina libraries for NGS, which I assume is many of you, I’d like to direct you to this new paper by Sheila Fisher’s group at the Broad Institute. In this paper Fisher describes the … Continue reading

Posted in bioinformatics, howto, methods, next generation sequencing | 1 Comment

Interpreting Population Genetics Formulae

Whether it’s simple equations like heritability (e.g., R = h2S or the ‘breeders equation’) or more complicated equations like Nei and Chesser’s (1983) unbiased estimator of HS, population genetics papers are filled with math. Early in my career I found … Continue reading

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Riding the Elephant

I recently received my first batch of reads from a single paired-end lane run on an Illumina Hi-Seq instrument. This batch totaled about 20 billion basepairs of DNA sequence, and the associated data files a combined 55.4 gigs of text. … Continue reading

Posted in bioinformatics, next generation sequencing, software | Tagged , , , , | 9 Comments

Surfing the Wave

As Dilara pointed out in her recent post, keeping track of all the new papers, programs, and techniques is an enormous challenge for the busy molecular ecologist. These days it seems that one should be following publications in Molecular Ecology, Molecular Ecology Resources (of course!), TrEE, Science, Nature, Ecology, PNAS, BMC Evolutionary Biology, and PLoS biology/genetics*. Of course, this doesn’t include those journals specific to your particular sub-discipline. – Finding New Papers –

The simplist way to keep track of new papers is with Google Reader. Google Reader, if you’re unaware, is google’s online Really Simple Syndication (RSS) reader. Basically, it lets you follow RSS feeds from searches on Pubmed, journals themselves, or blogs. In then colates on all the feed entries onto a single webpage. Essentially, you a list of journals and sublists with the most recent publications, abstracts, and links to the full articles. It definitely beats getting monthly table of contents emails.

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Posted in software | Tagged , , , , , , | 3 Comments