"Histone modifications directly modulate transcription factor binding to nucleosomes": codes for reviewers

Custom codes in R, Bash and Python for k-mer analysis of nucleosome-bound sequences: 1 - R_code_for_PIONEAR-seq_analysis_Figs_1BC_2BCEF_3AE_4ABF.R : R code for the analysis of sequencing files from the GEO repository GSE333423. This code was used to produce Table S4, main figures 1B-C, 2B-C/E-F, 3A/E and 4A-B/F, and supplementary figures S2-S6/S9/S11. 2 - README_Fig_3G.md: explanation and Bash commands to run the alignment analysis of AF3 models for PAX7 binding to free DNA VS nucleosomes that carry PAX7 HD motif at distinct positions. The bash commands call for the Python script 'Script_for_Fig_3G.py' to generate the Template modeling scores then depicted by the R code 'To_plot_Fig_3G.R'. 3 - Script_for_Fig_3G.py: This script uses the tool USalign to match the different AF3 models downloaded from the dataverse repo described in README_Fig_3G.md. It creates the csv file 'usalign_to_free_dna.csv' for PAX7 that the R code 'To_plot_Fig_3G.R' uses to generate the plot in figure 3G. 4 - To_plot_Fig_3G.R: This R code loads the csv file 'usalign_to_free_dna.csv' for PAX7 generated by 'Script_for_Fig_3G.py' to create the plot 'usalign_to_free_dna_dotplot.pdf' used in figure 3G and which depicts the alignment of the different DNA-bound PAX7 models generated by AF3. 5 - README_Fig_4E.md: explanation and Bash commands to run the alignment analysis of AF3 models for FOXA1 binding to free DNA VS nucleosomes that carry the DIV0 motif at distinct positions. The bash commands call for the Python script 'Script_for_Fig_4E.py' to generate the Template modeling scores then depicted by the R code 'To_plot_Fig_4E.R'. 6 - Script_for_Fig_4E.py: This script uses the tool USalign to match the different AF3 models downloaded from the dataverse repo described in README_Fig_4E.md. It creates the csv file 'usalign_to_free_dna.csv' for FOXA1 that the R code 'To_plot_Fig_4E.R' uses to generate the plot in figure 4E. 7 - To_plot_Fig_4E.R: This R code loads the csv file 'usalign_to_free_dna.csv' for FOXA1 generated by 'Script_for_Fig_4E.py' to create the plot in figure 4E and which depicts the alignment of the different DIV0-bound FOXA1 models generated by AF3. 8 - README_Fig_4H.md: explanation and Bash commands to run the SASA analysis for the 8-mers in the internal DNA region (from 60 to 81 bp) of a nucleosome core particle modeled by AF3 using a 147-bp W601 sequence. The bash commands call for the Python script 'Script_for_Fig_4H.py' to generate the SASA values then depicted by the R code 'To_plot_Fig_4H.R'. 9 - Script_for_Fig_4H.py: This script uses the Python library Bio.PDB.SASA to compute the Shrake-Rupley Solvent Accessibility Surface Area (SASA) of the the different 8-mers along the single-gyre region (from bp 60 to bp 81) around the dyad of a nucleosome core particle. It creates the csv file "w601_8mer_sasa.csv" that the R code 'To_plot_Fig_4E.R' uses to generate the plot in figure 4E. 10 - To_plot_Fig_4H.R: This R code loads the csv file "w601_8mer_sasa.csv" generated by 'Script_for_Fig_4E.py' to create the plot in figure 4E which depicts the SASA values of the different 8-mers along the single-gyre region (from bp 60 to bp 81) around the dyad of a nucleosome core particle. 11 - README_BASH_commands_to_generate_data_for_Fig_4J.md : Bash commands for the analysis of matches for CEBPB and OCT4 PWMs in genomic nucleosomes stratified by their overlap to H3K27ac marks. This code was used to produce the data that will generate Fig 4J. 12 - Rscript_plot_motif_rate_Fig_4J.R: uses the output of README_BASH_commands_to_generate_data_for_Fig_4J.md to plot Fig. 4J and to calculate Fisher tests for the two sets (namely, CEBPB and OCT4).