Non-consensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning

Workflow description, complete results and additional visualization for the publication Non-consensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.

In atac_analysis_source_codes.zip and sequence_analysis_source_codes, the scripts and Jupyter notebooks used to perform the analysis are stored.

In sequence_analysis.zip, results of sequence composition analysis can be found, together with results of the analysis of TF affinity using the HOCOMOCO database and figures describing predicted DNA shape around the binding site.

In atac_analysis_results.zip, visualization of GC content and incidence with ATAC-seq peaks in the same cell lines can be found.

The chosen_bed_files__thresholded.csv contains information on the ChIP-seq experiments used during the analysis.