Thursday, 10 November 2016

Installing Trinity on Mac OS X via homebrew -- update

A couple of months ago I wrote a short post about how I managed to install the RNA assembler Trinity on Mac OS X (El Capitan), on the off-chance it would be useful to someone else.

This morning I received an email from my friend Mazlina, who I worked with in London, saying she had been trying to do just that and had coincidentally stumbled on my post*. However it hadn't worked out quite as easily for her as it had for me.

It turned out to be due to a Java version problem. While 1.8 was installed, brew --config claimed that only 1.6 was, which is insufficient for Trinity installation.

Here's how she solved it, quoting from her email:

"First, I did
brew doctor
and just cleared up whatever it told me to [...]

$ brew doctor
Your system is ready to brew.

So by running
brew cask search java
it lists down the available java versions (the one you have, 8, is just java), and I went with 9-beta because that was the only one I could download at that time. And when I ran 

$ brew cask install java9-beta
$ brew install trinity
worked like a charm.

Not sure if that's exciting enough to go on the blog, but it solves it anyway."

(For reference, as I told her, given the average excitement level of the blog this should fit right in!)

* I'm never really sure whether these posts are read or not (as the stats from Blogger are always inflated by scanning bots) apart from when people let me know they've seen them - so if you ever bump in to me at a conference or something and have found one of them useful or interesting please let me know, I love to hear about it!

Friday, 4 November 2016

Cheap protocol for DNA extraction from agarose

I've just stumbled across this lovely paper from Sun et al., which reports a delightfully cheap and simple technique for extracting DNA from agarose gel slices.

Basically it's straightforward as poking a hole in the bottom of a .5 ml microcentrifuge tube, then nesting that inside a 1.5 ml tube. Some cotton or glass wool then goes in the bottom of the .5 ml tube, with your agarose slice containing your excised DNA band on top, and you just spin it through;  apparently the agarose gets retained on the wool and the aqueous phase gets spun to the lower compartment.

DNA gel extraction kits aren't the most expensive thing you're likely to buy (at about £1.50/$2 per tube), but if you do them occasionally it might be worth trying it out for the time saving: if you are doing lots regularly, it might well save a pretty penny.