This repository contains the code used to process all the data and reproduce the results and figures from the manuscript "Enhancers display constrained sequence flexibility and context-specific modulation of motif function".
For more information, see the manuscript:
Enhancers display constrained sequence flexibility and context-specific modulation of motif function
Franziska Reiter*, Bernardo P. de Almeida*, Alexander Stark. bioRxiv
* Equal contribution.
The raw sequencing data are available from GEO under accession number GSE211659.
The data necessary to reproduce all results and figures are available on zenodo at https://doi.org/10.5281/zenodo.7010528. Please download the respective datasets and follow the scripts below.
Random 8nt variants tested at seven enhancer positions in Drosophila S2 cells
- Pipeline for mapping sequencing reads
- R markdown to reproduce results
- Results in html
Systematic pasting of Drosophila TF motifs in hundreds of enhancer positions
- Sequencing reads were processed as in here
- R markdown to reproduce results
- Results in html
Systematic pasting of human TF motifs in hundreds of enhancer positions
- Sequencing reads were processed as in here
- R markdown to reproduce results
- Results in html
If you have any questions/requests/comments please contact me at [email protected].