ChIP-seq Working With Peaks - practical

In this practical we will read in two replicate sets of peaks from the Myc Encode dataset,filter by fold enrichment over input and find the number of peaks common to both replicates and those unique to either.

• First read in each of the Mel replicate peak sets found in MacsPeaks directory and create a GRanges object containing peak locations for each.

Now you have your peak sets as GRanges, you can start to work with the peaks in R.

• Find the number of peaks in each replicate.

• Find the number of peaks in each replicate on chromosome 4.

• Find the number of peaks on chromosome 4 which have a 5 fold enrichment above input.

Now we can use our GRanges to identify the peak in common or unique to replicates.

• Find the number of replicate 1 peaks common between replicates.
• Find the number of unique peaks in replicate 1

For a bonus question.

• Create a new GRanges of the summit locations from Mel Myc Peaks replicate 1.