Pre-course Material

The three first part from the UNIX Tutorial for Beginners

• Introduction
• chapter 1
• chapter 2

You must use http://uppnex.se/emu/ (or this mirror) to try the commands in the tutorial, otherwise the commands will not work. If you any questions regarding this tutorial contact: martin.dahlo@scilifelab.uu.se

Using Linux is often the hardest part of the course, so being familiar with writing things on a command-line will help. You should at least go through the exercises in the tutorial, no need to know it by heart.

Here are links to some manuals. You don’t have to read through all of it, but you should get a glimps of what it will be like to use the software. The top three are discussion fora, which could be useful to answer questions that are not covered by the manuals.

Biosupport.se: http://biosupport.se/
Biostar: http://www.biostars.org/
SeqAnswers: http://seqanswers.com/

Trinity: http://trinityrnaseq.sourceforge.net/
Cufflinks: http://cufflinks.cbcb.umd.edu/
Satuma/Spines: http://www.broadinstitute.org/science/programs/genome-biology/spines
Allpaths-lg: http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
blat: http://genome.ucsc.edu/goldenPath/help/blatSpec.html
blast: http://www.ncbi.nlm.nih.gov/books/NBK1763/