```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Homework 5

For each of these questions, show the commands you would use to answer the question, If the answer can be shown in less than 5 lines, show the answer as well.

### Question #1
Create a BED file representing all of the intervals in the genome that are NOT exonic.

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### Question #2

What is the average distance from GWAS SNPs to the closest exon? (Hint - have a look at the `closest` tool.)

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### Question #3
Count how many exons occur in each 500kb interval (“window”) in the human genome, what is the average value? (Hint - have a look at the `makewindows` tool.)

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### Question #4
Are there any exons that are completely overlapped by an enhancer? If so, how many?

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### Question #5
What fraction of the GWAS SNPs are exonic?

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### Question #6
What fraction of the GWAS SNPs lie in either enhancers or promoters in the hESC data we have?

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### Question #7
Create intervals representing the canonical 2bp splice sites on either side of each exon (don’t worry about excluding splice sites at the first or last exon). (Hint - have a look at the flank tool.)

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### Question #8
Which hESC ChromHMM state (e.g., `11_Weak_Txn`, `10_Txn_Elongation`) represents the most number of base pairs in each of chromosome 19 and chromosome 8?

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