Ashley Woodfin
A majority of ChIP-seq analysis can be automated freeing you up to focus on more custom based questions. This is a collection of scripts to automate ChIP-seq with many tasks related to transcriptional pausing analysis. Some tasks include selecting transcripts with the highest coverage in the TSS, making heat maps and average profile plots for defined regions or for genes stretched to the same length, looking at coverage across regions, and calculating and visualizing PolII pausing indexes.