Updated .gitignore to ignore ALL files by default. This resolves the problem of git tracking large bioinformatic files that I can't foresee.
Specified file types to track, R and other scripts, as well as text and markdown files.

Changed 'trancriptome' project to 'AphTranscriptome' for better description and consistency with my [project list](http://johnstantongeddes.org/ecological%20genetics/2013/07/12/projects.html)

Started work on transcriptome assembly, with script to trim, clip and perform QC on FASTQ files.