Easing the pain of titration

NOTE:  This is a repost of an entry that I wrote for the molecularecologist.com. Quickly following up on Nick's post re: Illumina Library Prep, Travis Glenn pointed me towards a manuscript in Nature Protocols that proposes an alternative to the oft-grumbled-about process of titrating libraries for 454/Ion Torrent…

(Relatively) Easily get coverage for velvet assemblies

You can get kmer coverage from contigs assembled by velvet by parsing the kmer value from the output fasta header, but sometimes I want "actual" coverage for contigs or coverage across a specific subset of contigs. Here is a way to do this relatively painlessly (requires that you first download…

Beast in the cloud

We've been running beast and mrbayes on several data sets lately, generally using ec2 to help us run multiple analyses simultaneously. Along those lines, I was interested in getting beast (using the beagle-lib running on ec2, to take advantage of their GPU HPC options (what a load of acronyms!). Anyway…

A penny for your method: Plate sealers

NOTE:  This is a repost of an entry that I wrote for the molecularecologist.com. You may call them plate sealers, we call them "sticky-tops" (as opposed to the rubber plate sealers we use for PCR). Whatever you call them, they seal up 96- and 384-well plates so you can…

Get your protein

NOTE: This is a repost of an entry that I wrote for the molecularecologist.com. This weekend, I was doing a little work on one of our projects where we are using various cpDNA genes. I really needed to get a number of protein sequences from Genbank for the products…

A penny for your method: PCR cleanup

NOTE:  This is a repost of an entry that I wrote for the molecularecologist.com. Very rarely, in scientific research, do we get the opportunity to do less with more. As a result, one thing that we are good at is stretching a dollar. To (hopefully) contribute something back to…