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titleExercise 2 solution

I've put my output for each line in the comment area.

Code Block
languagebash
titlesolution
module load samtools                                     # if needed
samtools view -c yeast_pairedend_sort.bam chrIII         # total number of reads on this chromosome: 507015503
samtools view -c -F 0X04 yeast_pairedend_sort.bam chrIII # reads on this chromosome which are unmapped: 461113973

So the total proportion of reads that were unmapped on chromosome III is 461113973/5070 15503 or 90.9%1%, which is really high!  Only 10% ~10% of reads on this chromosome were able to be mapped to the genome.

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