## 9.9 Exercises

### 9.9.1 Quality control

1. Apply the fragment size estimation procedure to all ChIP and Input available datasets. [Difficulty: Beginner]

2. Visualize the resulting distributions. [Difficulty: Beginner]

3. How does the Input sample distribution differ from the ChIP samples? [Difficulty: Beginner]

4. Write a function which converts the bam files into bigWig files. [Difficulty: Beginner]

5. Apply the function to all files, and visualize them in the genome browser. Observe the signal profiles. What can you notice, about the similarity of the samples? [Difficulty: Beginner]

6. Use GViz to visualize the profiles for CTCF, SMC3 and ZNF143. [Difficulty: Beginner/Intermediate]

7. Calculate the cross correlation for both CTCF replicates, and the input samples. How does the profile look for the control samples? [Difficulty: Intermediate]

8. Calculate the cross correlation coefficients for all samples and visualize them as a heatmap. [Difficulty: Intermediate]

#### 9.9.1.1 Peak calling

1. Use normR to call peaks for all SMC3, CTCF, and ZNF143 samples. [Difficulty: Beginner]

2. Calculate the percentage of reads in peaks for the CTCF experiment. [Difficulty: Intermediate]

3. Download the blacklisted regions corresponding to the hg38 human genome, and calculate the percentage of CTCF peaks falling in such regions. [Difficulty: Advanced]

4. Unify the biological replicates by taking an intersection of peaks. How many peaks are specific to each biological replicate, and how many peaks overlap. [Difficulty: Intermediate]

5. Plot a scatter plot of signal strengths for biological replicates. Do intersecting peaks have equal signal strength in both samples? [Difficulty: Intermediate]

6. Quantify the combinatorial binding of all three proteins. Find the number of places which are bound by all three proteins, by a combination of two proteins, and exclusively by one protein. Annotate the different regions based on their genomic location. [Difficulty: Advanced]

7. Correlate the normR enrichment score for CTCF with peak presence/absence (create boxplots of enrichment for peaks which contain and do not contain CTCF motifs). [Difficulty: Advanced]

8. Explore the co-localization of CTCF and ZNF143. Where are the co-bound regions located? Which sequence motifs do they contain? Download the ChIA-pet data for the GM12878 cell line, and look at the 3D interaction between different classes of binding sites. [Difficulty: Advanced]

#### 9.9.1.2 Motif discovery

1. Repeat the motif discovery analysis on peaks from the ZNF143 transcription factor. How many motifs do you observe? How do the motifs look (visualize the motif logs)? [Difficulty: Intermediate]

2. Scan the ZNF143 peaks with the top motifs found in the previous exercise. Where are the motifs located? [Difficulty: Advanced]

3. Scan the CTCF peaks with the top motifs identified in the ZNF143 peaks. Where are the motifs located? What can you conclude from the previous exercises? [Difficulty: Advanced]