Codes used in the GATA3 analysis.
Rscripts: (1) 1_find_gat_atc_closest_to_peak_reversecomplement_ATC.Rmd R script to find the subsequences centered around the GAT/ATC motif that are closest to the peak centers. These subsequences are then fed to NPLB for denovo motif analysis at the GATA3 peak centers.
(2) 2_1_plot_freq_ofseqs_perspacer_permotif.Rmd R script to calculate the occurence of Pal, rPal and tandem motifs having spacers between 0-10 at the GATA3 peaks. The code searched along the nucleotide sequence of the GATA3 peaks, for the motifs and outputs motif frequency per fasta file.
(3) 2_find_single_tandem_pal_rpal_freq_per_peak.Rmd R script to calculate the occurence of Single, Pal, rPal and Tandem motifs at the GATA3 peaks. If the distance between 2 motifs is more than user input number of bases, then the each of the motif is assumed to be single motif
(4) 3_plotting_NPLB_output_asheatmap.Rmd Rscript to plot the NPLB output as a heatmap
(5) mapping_phastcons
convert_wigFix_to_starch.sh
map_phastcons.sh
Shell scripts to map Phastcons scores to the regions of interest (GATA3 peaks).