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In my career many of the questions that I have worked on are related to transcriptional elongation by Polymerase 2 (PolII). These typically involve looking at the distribution of a protein such as PolII or other marks indicative of elongation by ChIP-seq with respect to it's profile around a gene and how this changes or shifts in different conditions. Some of my other projects are related to enhancers, which are small distal regulatory elements containing sequence motifs that proteins can bind to that then interact with cofactors to boost transcription at the promoter. Enhancers are often characterized by ChIP-seq of histone marks or quantitative methods such as STARR-seq. These enhancer regions defined by ChIP-seq or STARR-seq are also studied in its relation to the nearest gene or changes in coverage in different conditions. I decided to break up the workflows that I provide here in the two categories below. Follow the links for script examples.
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Gene based tasks and work flows
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Region based questions