Author Archives: Nicholas Crawford

Getting started with Ultra Conserved Elements

Posted on 1 Oct, 2013 by Nicholas Crawford

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

Posted on 19 Sep, 2011 by Nicholas Crawford

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

Posted on 18 May, 2011 by Nicholas Crawford

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 →

Posted in population genetics | Leave a comment

Riding the Elephant

Posted on 7 Feb, 2011 by Nicholas Crawford

I recently received my first batch of reads from a single paired-end lane run on an [Illumina Hi-Seq](http://www.illumina.com/systems/hiseq_2000.ilmn) 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

Posted on 6 Oct, 2010 by Nicholas Crawford

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. Continue reading →

Posted in software | Tagged , , , , , , | 4 Comments