In todays session we will work with some of Kindey and HindBrain ATAC-seq data.

I have already produced a summarisedexperiment of counts and put this in the data directory.

data/KidneyBrainCounts.RData

ATAC-seq analysis

  1. Perform a differential ATAC-seq analysis of the Kidney samples versus the Brain sample and write out to FASTA the top differential 1000 ATAC-seq peaks up and down for kidney minus brain.

  2. Extract the sequences for the top up and down 1000 regions and submit to Meme-ChIP.

  3. Perform a chromVar analysis on our Brain and Kidney data and plot the most variable motifs in a heatmap.