The course machines are named: ibv-course01.hpc.uio.no

## IGV VIA SSH FOR UNIX LAPTOPS (LINUX & MAC OSX)
When starting IGV you can use the ThinLink but there are some problems with dialog boxes . An alternative is to login directly via ssh and then start up IGV. For this to work you need to used the -X option
ssh -X username@ibv-course01.hpc.uio.no
Then once you are logged in, you start IGV using:
/share/inf-biox121/IGV_2.3.81/igv.sh
    
    
## READING THE HELPFUL MANUAL 
To get help on the options of a command use man command. For example:
    man grep
    
## DIRECTORIES OVERVIEW
slides >> slides for the course
inputData >> reference genome and read sets
exerDefinitions >> the exercise scripts
exerSandbox >> where you do the exercises

## SLIDE UPDATES
Updated slides are on the website at: https://github.com/lexnederbragt/INF-BIOx121/blob/2016/Variant_calling/index.md
Updated slides can be found on the central location /data/vc/slides
You can copy these to your vc directory by using for example:
source /data/vc/exerDefinitions/setupEnv.bash
/data/vc/exerDefinitions/copyFiles.bash

## AWK
awk 'BEGIN{OFS="\t"; FS="\t";};{print $8};END{}'


## GETTING HOLD OF PRE-COMPUTED RESULTS
cp -r /data/vc/exerResults/02_basicPipeline/* vc/exerSandbox/02_basicPipeline/