In the last two modules, we have learned about DNA sequence motifs and their applications. In this module, we will use the tool HOMER to identify motifs in ChIP-seq data. Before class, please view the lecture "Transcriptional Regulatory Analysis" (link to lecture on mediasite and lecture slides are on Canvas) and answer the following questions.
1) What are two challenges to ChIP-seq peak calling?
2) What is in the first three columns of a file in BED format?
3) How does identifying transcriptional networks help to connect transcription factors to genes they may regulate?