Exercises:

Use files from 
/cluster/scratch/michalo/public

Linux re-fresh:

* connect with SSH to Euler
* create a folder in your $HOME
* create a folder in your $SCRATCH
* create a file (touch) and edit the content
* copy file to your laptop, edit it, copy back to Euler

Bash:

* Login to Euler
* Create the bash script displaying "Hello world!"
* Run the script
* Use the command line parameters to display "Hello world, I am ..."
* Create and run a script that modifies (copy, content change, etc) a file or several files


Genomic formats and AWK:

* Try and modify the all examples from the AWK slides 

Genomic software:

* align the mini.fastq to the human reference genome using bowtie, create a BAM file
* align the mini.fastq to the human reference genome using bowtie, create a SAM file
* convert the SAM to BAM using samtools
* using samtools, sort and index the BAM
* find the transcripts in the BAM using cufflinks
* on which chromosome are the discovered transcripts?
* do the discovered transcripts overlap?
* count the reads in genes using featureCounts and human GTF annotation
* which genes have counts?


RNA-seq with R:

* Follow the R analysis from the jupyter notebook in terminal, RStudio or juyter