RNAseq_workshop

Protocol and other material for RNAseq workshop (Illumina + some long read).

why latex

we now have both a) syntax highlighting and b) the ability to copy paste from code blocks and get valid commands.

I'd give them a printed version only until they are through the linux section, and after that they can have the pdf as well.

to make the pdf (needs texlive, and probably texlive-extra-utils)

pdflatex RNAseqWorkshop.tex

support files

RNAseqWorkshop.tex imports everything in sections. So for instance, all of the content of the biological data extraction section is organized in "sections/03_biological_data_extraction.tex".

As this section had a lot of code, it currently imbeds scripts from "R/". But that can definitely be changed if desired.

support scripts for the course

The course uses a few scripts from us that should be put in the $PATH for the .py scripts under "python/".

The exception to this is the join_r_scripts.py in the main directory, which just creates "musings.R", which should be provided in the RNAdata directory the way the script is written (although since we can now copy paste from the pdf when latex/listings is used, we have the theoretical option to drop this).