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Simple hands-on exercise on genomic alignment. 
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The goal is to test how many alignments will the BWA aligner find on a reference genome
(Arabidopsis Arenosa) using an input file of 100'000 Illumina reads. 

Make a copy of the input file and the reference genome with index into your home 
directory. 
Write the short script and send it to slurm queue. 
Check how many alignments you have got in the SAM alignment file. 


input:
/cluster/scratch/michalo/public/test.fastq

reference genome with a pre-built BWA index:
/cluster/scratch/michalo/public/aarenosa.fa

Module needed:
module load gcc/4.8.2 gdc bwa/0.7.17


BWA aligner manual
https://bio-bwa.sourceforge.net/bwa.shtml