| Due: 5pm on Feb 16

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/chr1.hg19.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

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

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).

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.

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')

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.

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