Starting a new page for exercises

exercises.md

+# Exercises
+
+## Quality control
+
+1. Add a rule that generates [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) reports for the two input fastq.gz files.
+   * The tool `fastqc` is available from the `bioconda` conda channel.
+   
+   * An example command-line to use `fastqc` is
+   
+     ```
+     $ fastqc chip-seq/H3K4-TC1-ST2-D0.12.fastq.gz
+     ```
+   
+   * The output are two files in the same directory as the input file, `H3K4-TC1-ST2-D0.12_fastqc.html` and `H3K4-TC1-ST2-D0.12_fastqc.zip`.
+   
+   * You might want to copy at least the html file to the `output` directory.
+   
+   * Do not forget to add at least one of the output files to the summary rule or explicitly specify it on the command-line.
+   
+2. Add a rule that generates alignment statistics for the two bam files with [Picard](https://broadinstitute.github.io/picard/) [CollectAlignmentSummaryMetrics](https://broadinstitute.github.io/picard/command-line-overview.html#CollectAlignmentSummaryMetrics).
+
+   * The tool `picard` is available from the `bioconda` conda channel.
+   
+   * An example command-line to run `picard` is
+   
+     ```
+     $ picard CollectAlignmentSummaryMetrics R=reference/Mus_musculus.GRCm38.dna_sm.chromosome.12.fa I=bowtie2/H3K4-TC1-ST2-D0.12.bam O=output/alignment_metrics_H3K4-TC1-ST2-D0.txt
+     ```
+   
+   * You can use the `params` directive again to specify the reference file.
+