Problem Set 2

| Due: 5pm on Feb 16

Workflow

See here for the general workflow.

Your answers should be in YAML format in a file called answers.yml at the top level of the repository.

# answers.yml should look like this:
answer-1: 123
answer-2: 456

For this problem set you will use BEDtools to do some calculations. Each problem is worth 10 points.

These files are in the data/ directory.

• Fasta file with human genome sequence: fasta/hg19.chr22.fa
• BED file containing ChIP-seq peaks for H3K4me3 in Hela cells: bed/encode.h3k4me3.hela.chr22.bed.gz
• BED file with all genes in hg19: bed/genes.hg19.bed.gz.
• File containing peak calls for ENCODE transcription factor ChIP-seq experiements: bed/encode.tfbs.chr22.bed.gz.
• Bedgraph with CTCF ChIP-seq data in bedGraph format: bedgraph/ctcf.hela.chr22.bg.gz
• A "genome file" with chromosome size info: genome/hg19.genome
• A file containing transcription start sites (TSS) for chr22: bed/tss.hg19.chr22.bed.gz

Question 1

Use BEDtools intersect to identify the size of the largest overlap between CTCF and H3K4me3 locations.

Question 2

Use BEDtools to calculate the GC content of nucleotides 19,000,000 to 19,000,500 on chr22 of hg19 genome build. Report the GC content as a fraction (e.g., 0.50).

Question 3

Use BEDtools to identify the length of the CTCF ChIP-seq peak (i.e., interval) that has the largest mean signal in ctcf.hela.chr22.bg.gz.

Question 4

Use BEDtools to identify the gene promoter (defined as 1000 bp upstream of a TSS) with the highest median signal in ctcf.hela.chr22.bg.gz. Report the gene name (e.g., 'ABC123')

Question 5

Use BEDtools to identify the longest interval on chr22 that is not covered by genes.hg19.bed.gz. Report the interval like chr1:100-500.

Question 6 (extra credit)

Use one or more BEDtools that we haven't covered in class. Be creative.