Cannibal Lobsters and Climate Change

We headed north yesterday to wander around Pelham Bay Park and City Island in the Bronx. The main attraction of City Island seems to be lobster restaurants, and I assumed the former owner of the tail I ate was caught in nearby Long Island Sound. It seems though that the local lobster industry has been on the decline for years with disease or changes to the ecosystem to blame. Here’s more information on the threat of climate change to the lobster industry, courtesy of Climate Desk:

Powerful Photo of the Effects of Elephant Poaching

This compelling photo was recently posted to the Facebook page of the Kenya Wildlife Service:

Some internet sleuthing reveals the photographer to be Nick Brandt, and his website is worth the trip for other amazing shots of African savannah wildlife (and a mountain gorilla or two for good measure). The baboons from Amboseli are of particular interest to me. The Amboseli basin is the site of a well-known primate hybrid zone similar to the one in Ethiopia 800 miles to the north which is the subject of my in-progress Ph.D. thesis.

Removing Adaptors from Next-Gen Data

I had a lot of adapter contamination in a recent ddRADseq Illumina PE HiSeq run and toyed around with a bunch of programs to get rid of it. These two guides in particular were super helpful, so I’m linking to them here for the benefit of others (and future me!) who find themselves in the same predicament.

I ended up using FastqMcf using the adapter (adaptor? adapt[eo]r?) sequences gathered with this simple Unix one-liner, stolen from the second link:

curl -s http://www.omicsoft.com/downloads/ngs/contamination_list/v1.txt 2>&1 | \
sed "/^\s\+$/d;s/\t\+/\t/g;s/ /_/g;s/,//g;s/'//g" | \
awk '{print ">"$1; print $2;}' > adaptors_list.fa 

This has been a fairly technical post, so here’s a picture of a cute primate to make it more interesting. It’s a galago in honor of my good friend who just defended his dissertation. Glückwünsche, Luca!

Moholy-Galago

(Galago moholi photo by Flickr user Joachim S. Müller.)