This repository contains the scripts and pipelines used in the manuscript "Functional maps of a genomic locus reveal confinement of an enhancer by its target gene" by Eder et al.
In this study we investigated the Sox2 genomic locus in mESCs to better understand the positional relationship between the mouse Sox2 gene and its distal enhancer. We created high-resolution functional maps of the locus by relocating different Sox2-reporters to >1,000 alternative positions.
This repository contains information about
- Tagmentation: Tn5_tagmentation mapping (pipeline)
- including all config files used for the data in the paper
- Analysis:
- assignment of locations to clones (between Tagmentation mapping and figure generation)
- some annotation tables (in Data)
- CTCF ChIP seq analysis
- General functions: includes the calculation of expression score
- Figures: R markdown files to create paper figures