Simplified and corrected some of the RNA-seq module.
Added introductory section on FASTQ quality value encoding. This always
causes confusion in the workshop, so having this info in the handout
should be beneficial.
Added code to make the workshop's data directory contents owned by the
sudoer user specified with the -s argument (defaults to ubuntu). This
means that scp'ing files to VM's is possible using the ubuntu
user.
Added empty skipped.gtf cufflink result files.
Updated workshop deployment script content and location.
Added a complete example of a BASH script used for setting up the NGS
workshop in Adelaide.
Added example usage of the environments.
Moved custom LaTeX commands to a separate btp.sty file and defined a few
convenient set* commands for workshop and module info. Now simply do
\usepackage{btp} or \usepackage[trainermanual]{btp} to generate the
trainee and trainer styled versions of the handout.
Added Workshop setup information to a subdirectory.
Updated location for Canberra workshop
Store the PDFs as pat of the repo.
Added alternating row colours.
Updated the PDfs to reflect LaTeX commits.
Removed date and location specifics from the front cover.
Added language styling for R and command syntax.
Updated the PDFs.
Ran dos2unix.
A few minor updates.
Fixed typos.
Updated mouse from mm9 to mm10
1) updated mm9 references to mm10
2) Updated IGV 2.1 references to IGV 2.3
Updated PDFs.