/dSMF_analysis_at_dm_enhancer

Primary LanguageShellMIT LicenseMIT

dual Enzyme Single Molecule Footprinting (dSMF) analysis at Drosophila Enhancers

Data and scripts to generate figure panels

Figure 4

Panel A: percentage methylation distribution in open and closed enhancers

Data:

  • data/figure4/panel_a/open_enh.tsv.gz
  • data/figure4/panel_a/closed_enh.tsv.gz
$ cd data/figure4/panel_a/
$ gunzip open_enh.tsv.gz 
$ gunzip closed_enh.tsv.gz
$ cd - 
$ Rscript scripts/plot_percentage_methylation_on_reads.R \
  data/figure4/panel_a/open_enh.tsv \
  data/figure4/panel_a/closed_enh.tsv \
  4 \
  5 \
  figures/figure4/panel_a/open_vs_closed.dist.pdf \
  figures/figure4/panel_a/open_vs_closed.dist.png \
  figures/figure4/panel_a/open_vs_closed.smooth.dist.pdf \
  figures/figure4/panel_a/open_vs_closed.smooth.dist.png \
  figures/figure4/panel_a/open_vs_closed.ecdf.pdf \
  figures/figure4/panel_a/open_vs_closed.ecdf.png \
  figures/figure4/panel_a/open_vs_closed.cnt.pdf \
  figures/figure4/panel_a/open_vs_closed.cnt.png \

Panel B: Example footprints

Panel C, D: Footprints

Data:

MNase data: data/figure4/panel_c_and_d/mnase_data.tsv

  • Methylation vector:
  • With sam flag 83-163: data/figure4/panel_c_and_d/mvec_83_order.tsv
  • With sam flag 99-147: data/figure4/panel_c_and_d/mvec_99_order.tsv
  • Footprint vector:
  • With sam flag 83-163: data/figure4/panel_c_and_d/83_order.tsv
  • With sam flag 99-147: data/figure4/panel_c_and_d/99_order.tsv

First order footrpints based on footprint length and location and then plot:

$ cd data/figure4/panel_c_and_d/ 
$ sh order_by_flen_and_loc.sh 
$ gnuplot  peak_229_3_methylation.gplt 
$ gnuplot  peak_229_3_footprint.gplt

Panel E: Obs vs expected footprint length distribution in open and closed enhancers

Data:

  • Observed (Open): data/figure4/panel_e/open_130_5bp.hist
  • Observed (Closed): data/figure4/panel_e/closed_130_5bp.hist
$ gnuplot data/figure4/panel_e/obs_vs_expected.gplt

Panel F: Percentage occupancies of Naked, TF, and Nucleosome

Data:

  • data/figure4/panel_f/occupancy_open.tsv
  • data/figure4/panel_f/occupancy_closed.tsv
$ Rscript scripts/bxplt_violin.R

Panel G: K-means on occupancy matrix

Data:

  • data/figure4/panel_g/open_peaks_nclust_3.ori.tsv
$ gnuplot data/figure4/panel_g/open_peaks.ori.complete.gplt

Panel H: Boxplot of k-means occupany by states

Data:

  • data/figure_4/panel_h/open_peaks_nclust_3.ori.tsv
$ Rscript scripts/boxplt_by_state.R

Panel I: MNase log2(Short/Long) heatmap in k-means clusters

Data:

  • data/figure4/panel_i/open_all_peaks_log2_1kb.csv.gz
$ gnuplot data/figure4/panel_i/1kb_all_log2_plot.plt

Figure 5

Panel A: DNA molecule count distribution

Data:

  • data/figure5/panel_a/cobinding_data_with_normalized_extent_of_cobinding.tsv
$ Rscript scripts/cobinding_dna_molecule_count_distribution.R data/figure5/panel_a/cobinding_data_with_normalized_extent_of_cobinding.tsv

Panel B:

Panel C: Cobinding example plot

Data:

  • Methylation vector: data/figure5/panel_c/peak_110_4_dist_78/peak_110_4_dist_78_nine_state_mvec.tsv
  • Footprint vector: data/figure5/panel_c/peak_110_4_dist_78/peak_110_4_dist_78_nine_state_fp.tsv
$ cd data/figure5/panel_c/peak_110_4_dist_78/
$ sh ../scripts/plot_all.sh peak_110_4_dist_78

Figures are found in:

  • data/figure5/panel_c/peak_110_4_dist_78/peak_methylation.pdf
  • data/figure5/panel_c/peak_110_4_dist_78/peak_footprint.pdf

Panel D: Six state ccupancy boxplots

Data:

  • data/figure5/panel_d/cobinding_data_six_states.tsv
$ Rscript scripts/boxplt_cobinding_six_states.R data/figure5/panel_d/cobinding_data_six_states.tsv

Figure 6

Panel A: extent of co-binding analysis

Data:

  • data/figure6/panel_a/normalized_extent_of_cobinding.tsv
$ Rscript scripts/phyper_extent_of_cobinding.R data/figure6/panel_a/normalized_extent_of_cobinding.tsv

Panel B: Frequnecy of number of enhancers with co-binding events

Data:

  • data/figure6/panel_b/cobinding_frequency_at_enh.tsv
$ cd data/figure6/panel_b
$ gnuplot barplt.gplt

Panel C: Peak distance distribution agiainst extent of co-binding

Data:

  • data/figure6/panel_c/dist_(1,2,3,4).hist
$ cd data/figure6/panel_c
$ gnuplot line_plot.gplt

Panel D: Boxplot of occupancies for different classes of co-binders

Data:

  • data/figure6/panel_d/imb_with_occupancy_data.tsv
$ cd data/figure6/panel_d
$ Rscript three_groups.R
$ cd plots_imb

Panel E and F: ChIP and CATCH-IT analysis

Data:

  • data/figure6/panel_e_and_f/
$ cd data/figure6/panel_e_and_f/ 
$ Rscript Analysis_wFlag_clean.R