diff --git a/src/commands.sh b/src/commands.sh
new file mode 100644
index 0000000000000000000000000000000000000000..5d47f4700dee534fce2240d64bc6809c4dc8ddfd
--- /dev/null
+++ b/src/commands.sh
@@ -0,0 +1,764 @@
+#!/bin/bash
+
+python3 -m src.bed_handler
+python3 -m src.bed_handler.filter_bed \
+  --bed_file data/bed/gene.bed \
+  --filter_file data/gene_5-3_loop_tot.txt \
+  --col_name 'id' \
+  --outfile gene_with_5-3p_loop_tot.txt
+
+python3 -m src.bed_handler.filter_bed \
+  --bed_file data/bed/gene.bed \
+  --filter_file data/gene_5-3_loop_ctrl.txt \
+  --col_name 'id' \
+  --outfile gene_with_5-3p_loop_ctrl.txt
+
+python3 -m src.bed_handler.filter_bed \
+  --bed_file data/bed/gene.bed \
+  --filter_file data/gene_5-3_loop_siPPdown.txt \
+  --col_name 'id' \
+  --outfile gene_with_5-3p_loop_siPPdown.txt
+
+python3 -m src.bed_handler.filter_bed \
+  --bed_file data/bed/gene.bed \
+  --filter_file data/gene_without_5-3_loop_siPPdown.txt \
+  --col_name 'id' \
+  --outfile gene_without_5-3p_loop_siPPdown.txt
+
+python3 -m src.bed_handler.filter_bed \
+  --bed_file data/bed/gene.bed \
+  --filter_file data/gene_without_loops_siPPdown.txt \
+  --col_name 'id' \
+  --outfile gene_without_loops_siPPdown.txt
+
+mkdir results/figures
+
+array=(all_replicates rep1 rep2 rep3)
+for myrep in ${array[*]}; do
+	python3 -m src.visu \
+		--design data/design_exp_${myrep}.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed results/bed_file/filtered_gene.bed \
+		--region_name gene \
+		--output results/figures/  \
+		--border_name TSS TTS \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm 'None'
+
+	python3 -m src.visu \
+		--design data/design_exp_${myrep}.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed results/bed_file/filtered_gene.bed \
+		--region_name gene \
+		--output results/figures/  \
+		--border_name TSS TTS \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm '0'
+	mv results/figures/metagene_gene_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/metagene_gene_100bin_10000_nt-around-25-bin_b0_norm_${myrep}.pdf
+	mv results/figures/metagene_gene_100bin_10000_nt-around-25-bin.pdf results/figures/metagene_gene_100bin_10000_nt-around-25-bin_${myrep}.pdf
+done
+
+
+
+array=(all_replicates rep1 rep2 rep3)
+for myrep in ${array[*]}; do
+	python3 -m src.visu \
+		--design data/design_exp_${myrep}.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt \
+		--region_name gene \
+		--output results/figures/  \
+		--border_name TSS TTS \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm 'None'
+
+	python3 -m src.visu \
+		--design data/design_exp_${myrep}.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt \
+		--region_name gene \
+		--output results/figures/  \
+		--border_name TSS TTS \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm '0'
+	mv results/figures/metagene_gene_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/metagene_gene_100bin_10000_nt-around-25-bin_b0_norm_${myrep}_5-3-loop.pdf
+	mv results/figures/metagene_gene_100bin_10000_nt-around-25-bin.pdf results/figures/metagene_gene_100bin_10000_nt-around-25-bin_${myrep}_5-3-loop.pdf
+done
+
+
+for gene_bed in $(ls results/bed_file/CTCF*gene.bed); do
+	exon_bed=${gene_bed/gene/exon}
+	exon_name=(${exon_bed//\// })
+	full_name=${exon_name[-1]/.bed/}
+	full_name=${full_name/exon/gene-dup}
+	file_name=${exon_name[-1]/.bed/}
+	gene_bed=${gene_bed/.bed/-dup.bed}
+
+	python3 -m src.visu \
+		--design data/design_exp_all_replicates.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed ${exon_bed} \
+		--region_name exon \
+		--output results/figures/  \
+		--border_name start_exon end_exon \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm 'None'
+	mv results/figures/metagene_exon_100bin_10000_nt-around-25-bin.pdf results/figures/${file_name}_metagene_exon_100bin_10000_nt-around-25-bin.pdf
+
+	python3 -m src.visu \
+		--design data/design_exp_all_replicates.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed ${gene_bed} \
+		--region_name gene \
+		--output results/figures/  \
+		--border_name start_exon end_exon \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm '0'
+	rm results/figures/metagene_gene_100bin_10000_nt-around-25-bin_b0_norm.pdf 
+
+	python3 -m src.visu \
+		--design data/design_exp_all_replicates.txt \
+		--bw_folder data/bigwig/ \
+		--region_bed ${exon_bed} \
+		--region_name exon \
+		--output results/figures/  \
+		--border_name start_exon end_exon \
+		--environment 10000 25 \
+		--show_replicate n \
+		--figure_type metagene \
+		--nb_bin 100 \
+		--norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${full_name}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+	mv results/figures/metagene_exon_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/${file_name}_metagene_exon_100bin_10000_nt-around-25-bin_file_norm.pdf
+	
+
+done
+
+########################################################
+# Condition siPP/siCTRL - exon ddx_down vs exon ddx_down_ctcf #
+########################################################
+# exon ddx_down_ctcf corresponds to exons down-regulated by ddx5/17 near a ctcf site and
+# exon ddx_down corresponds to exons down-regulated by ddx5/17 far from ctcf sites
+
+exps=(siCTRL siDDX)
+for exp in ${exps[*]}; do
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_gene.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_gene.bed \
+	--region_name ddx_down_ctcf ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "None"
+
+mv results/figures/metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/exp_${exp}_metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_gene.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_gene.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_gene.bed \
+	--region_name ddx_down_ctcf ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+mv results/figures/metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_${exp}_metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_b0_norm_gene.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_gene-dup.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_gene-dup.bed \
+	--region_name ddx_down_ctcf ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+rm results/figures/metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed \
+	--region_name ddx_down_ctcf ddx_down \
+	--output results/figures/  \
+	--border_name start_exon end_exon \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "results/figures/coef_table/tmp_cov_table_design_exp_${exp}_CTCF_2000_both_ddx_down_with0_gene-dup-Far_CTCF_2000_both_ddx_down_with0_gene-dup_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+
+mv results/figures/metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/exp_${exp}_metagene_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_file_norm_exon.pdf
+done
+
+########################################################
+# Condition siPP and siCTRL - ddx_down_5-3              #
+########################################################
+
+python3 -m src.visu \
+	--design data/design_exp_all_replicates.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt \
+	--region_name ddx_down_5-3 \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+mv results/figures/metagene_ddx_down_5-3_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_all_metagene_ddx_down_5-3_100bin_10000_nt-around-25-bin_b0_norm_gene.pdf
+
+########################################################
+# Condition siPP - ddx_down_5-3 vs exon ddx_down #
+########################################################
+# gene ddx_down_5-3 corresponds to genes containing at least one exons down-regulated by ddx5/17 and having a 5'-3' loop and
+# gene ddx_down corresponds to genes containing exons down-regulated by ddx but without a 5'-3' loop
+
+
+python3 -m src.visu \
+	--design data/design_exp_siDDX.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+	--region_name ddx_down_5-3 ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_siPP_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm_gene.pdf
+
+python3 -m src.visu \
+	--design data/design_exp_siDDX.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+	--region_name ddx_down_5-3 ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "None"
+
+mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/exp_siPP_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_gene.pdf
+
+rep=(1 2 3)
+for i in ${rep[*]}; do
+  python3 -m src.visu \
+    --design data/design_exp_siDDX_rep${i}.txt \
+    --bw_folder data/bigwig/ \
+    --region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+    --region_name ddx_down_5-3 ddx_down \
+    --output results/figures/  \
+    --border_name start_gene end_gene \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm "0"
+
+  mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_siPP_rep${i}_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_normgene.pdf
+done
+
+########################################################
+# Condition siCTRL - ddx_down_5-3 vs exon ddx_down #
+########################################################
+# gene ddx_down_5-3 corresponds to genes containing at least one exons down-regulated by ddx5/17 and having a 5'-3' loop and
+# gene ddx_down corresponds to genes containing exons down-regulated by ddx but without a 5'-3' loop
+
+python3 -m src.visu \
+	--design data/design_exp_siCTRL.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+	--region_name ddx_down_5-3 ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_siCTRL_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm_gene.pdf
+
+python3 -m src.visu \
+	--design data/design_exp_siCTRL.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+	--region_name ddx_down_5-3 ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "None"
+
+mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/exp_siCTRL_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_gene.pdf
+
+rep=(1 2 3)
+for i in ${rep[*]}; do
+  python3 -m src.visu \
+    --design data/design_exp_siCTRL_rep${i}.txt \
+    --bw_folder data/bigwig/ \
+    --region_bed results/bed_file/gene_with_5-3p_loop_siPPdown.txt results/bed_file/gene_without_loops_siPPdown.txt \
+    --region_name ddx_down_5-3 ddx_down \
+    --output results/figures/  \
+    --border_name start_gene end_gene \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm "0"
+
+  mv results/figures/metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_siCTRL_rep${i}_metagene_ddx_down_5-3-ddx_down_100bin_10000_nt-around-25-bin_b0_norm_gene.pdf
+done
+
+
+
+############################################################
+#     GC content exon ddx_down vs exon ddx_down_ctcf       #
+############################################################
+
+
+python3 -m src.gc_content -B results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed -b ddx_down ddx_down_ctcf -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 1000
+
+
+
+############################################################################
+# other Exon in genes containing an exon regulated by DDX
+############################################################################
+
+  ########################################################
+  # Condition siCTRL - exon ddx_down vs exon ddx_down_ctcf #
+  ########################################################
+
+
+
+python3 -m src.bed_handler.get_other_exon_in_same_gene -b results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed -d 2000 -o oexon_2000_CTCF_2000_both_ddx_down_with0_exon.bed
+python3 -m src.bed_handler.get_other_exon_in_same_gene -b results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed -d 2000 -o oexon_2000_Far_CTCF_2000_both_ddx_down_with0_exon.bed
+
+exps=(siCTRL siDDX)
+for exp in ${exps[*]}; do
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_gene.bed results/bed_file/oexon_2000_Far_CTCF_2000_both_ddx_down_with0_gene.bed \
+	--region_name other_ddx_down_ctcf other_ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "None"
+
+mv results/figures/metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/exp_${exp}_metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_gene.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_gene.bed results/bed_file/oexon_2000_Far_CTCF_2000_both_ddx_down_with0_gene.bed \
+	--region_name other_ddx_down_ctcf other_ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+mv results/figures/metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf results/figures/exp_${exp}_metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_gene_b0_norm.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_gene-dup.bed results/bed_file/oexon_2000_Far_CTCF_2000_both_ddx_down_with0_gene-dup.bed \
+	--region_name other_ddx_down_ctcf other_ddx_down \
+	--output results/figures/  \
+	--border_name start_gene end_gene \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "0"
+
+rm results/figures/metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf
+
+
+python3 -m src.visu \
+	--design data/design_exp_${exp}.txt \
+	--bw_folder data/bigwig/ \
+	--region_bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/oexon_2000_Far_CTCF_2000_both_ddx_down_with0_exon.bed \
+	--region_name other_ddx_down_ctcf other_ddx_down \
+	--output results/figures/  \
+	--border_name start_exon end_exon \
+	--environment 10000 25 \
+	--show_replicate n \
+	--figure_type metagene \
+	--nb_bin 100 \
+	--norm "results/figures/coef_table/tmp_cov_table_design_exp_${exp}_oexon_2000_CTCF_2000_both_ddx_down_with0_gene-gene-dup-oexon_2000_Far_CTCF_2000_both_ddx_down_with0_exon-gene-dup_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+
+mv results/figures/metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/exp_${exp}_metagene_other_ddx_down_ctcf-other_ddx_down_100bin_10000_nt-around-25-bin_file_norm_exon.pdf
+done
+
+
+###########################################################
+# Figures siPP vs siCTRL pour ddx_down_ctcf,
+# other_ddx_down_ctcf, ddx_down
+###########################################################
+
+list_names=(ddx_down_ctcf other_ddx_down_ctcf ddx_down)
+bed_names=(CTCF_2000_both_ddx_down_with0_exon.bed oexon_2000_CTCF_2000_both_ddx_down_with0_exon.bed Far_CTCF_2000_both_ddx_down_with0_exon.bed)
+for i in ${!list_names[*]}; do
+  cname=${list_names[i]}
+  bed=${bed_names[i]}
+  gbed=${bed/exon\.bed/gene-dup.bed}
+  nbed=${gbed/\.bed/}
+  python3 -m src.visu \
+      --design data/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig/ \
+      --region_bed results/bed_file/${gbed} \
+      --region_name ${cname} \
+      --output results/figures/  \
+      --border_name TSS TTS \
+      --environment 10000 25 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin 100 \
+      --norm '0'
+
+  rm results/figures/metagene_${cname}_100bin_10000_nt-around-25-bin_b0_norm.pdf
+
+  python3 -m src.visu \
+      --design data/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig/ \
+      --region_bed results/bed_file/${bed} \
+      --region_name ${cname} \
+      --output results/figures/  \
+      --border_name exon_start exon_stop \
+      --environment 10000 25 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin 100 \
+      --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+
+  mv results/figures/metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf
+done
+
+## Recap
+
+python3 -m src.visu \
+    --design data/design_exp_all_replicates.txt \
+    --bw_folder data/bigwig/ \
+    --region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_gene-dup.bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_gene-dup.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_gene-dup.bed \
+    --region_name ddx_down_ctcf other_ddx_down_ctcf ddx_down \
+    --output results/figures/  \
+    --border_name TSS TTS \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm '0'
+
+rm results/figures/metagene_ddx_down_ctcf-other_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_b0_norm.pdf
+
+python3 -m src.visu \
+    --design data/design_exp_all_replicates.txt \
+    --bw_folder data/bigwig/ \
+    --region_bed results/bed_file/CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/oexon_2000_CTCF_2000_both_ddx_down_with0_exon.bed results/bed_file/Far_CTCF_2000_both_ddx_down_with0_exon.bed \
+    --region_name ddx_down_ctcf other_ddx_down_ctcf ddx_down \
+    --output results/figures/  \
+    --border_name exon_start exon_stop \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm 'results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_CTCF_2000_both_ddx_down_with0_gene-dup-oexon_2000_CTCF_2000_both_ddx_down_with0_gene-dup-Far_CTCF_2000_both_ddx_down_with0_gene-dup_100bin_10000_nt-around-25-bin_bin0_norm.txt'
+
+mv results/figures/metagene_ddx_down_ctcf-other_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metagene_ddx_down_ctcf-other_ddx_down_ctcf-ddx_down_100bin_10000_nt-around-25-bin_file_norm.pdf
+
+
+###############################################################################
+#             Bigwig from MCF7 rnaseq
+###############################################################################
+
+# Create a bed file containing all gene containing one DDX-down exons
+echo -e "#ref\tstart\tend\tid\tscore\tstrand" > results/bed_file/ddx_down_gene.bed
+cat results/bed_file/CTCF_2000_both_ddx_down_with0_gene.bed \
+  results/bed_file/Far_CTCF_2000_both_ddx_down_with0_gene.bed | \
+  sort -u | \
+  grep -v "#ref" >> results/bed_file/ddx_down_gene.bed
+
+# Zoom on the 1500 pb at the beginning of the exons.
+python3 -m src.bed_handler.bed_resize \
+  -b results/bed_file/ddx_down_gene.bed \
+  -s 1500 \
+  -o ddx_down_gene_size1500.bed
+
+
+python3 -m src.visu \
+    --design data/bam_mcf7_rnaseq/design_exp_all_replicates.txt \
+    --bw_folder data/bam_mcf7_rnaseq \
+    --region_bed results/bed_file/ddx_down_gene.bed \
+    --region_name all_ddx_down \
+    --output results/figures/  \
+    --border_name TSS TTS \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm 'None'
+
+mv results/figures/metagene_all_ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/metagene_MCF_rnaseq_all_ddx_down.pdf
+
+
+python3 -m src.visu \
+    --design data/bam_mcf7_rnaseq/design_exp_all_replicates.txt \
+    --bw_folder data/bam_mcf7_rnaseq \
+    --region_bed results/bed_file/ddx_down_gene_size1500.bed \
+    --region_name all_ddx_down \
+    --output results/figures/  \
+    --border_name TSS TSS_1.5kb \
+    --environment 10000 25 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm 'None'
+
+mv results/figures/metagene_all_ddx_down_100bin_10000_nt-around-25-bin.pdf results/figures/metagene_MCF_rnaseq_all_ddx_down_tss1.5kb.pdf
+
+
+#### Readthrough
+
+# Create readthrough bed files
+python3 -m src.bed_handler.filter_bed -b data/bed/gene.bed -f data/readthrough_gene.txt -c score -o readthrough_gene.bed
+python3 -m src.bed_handler.filter_bed -b data/bed/gene.bed -f data/readthrough_gene.txt -c score -o no_readthrough_gene.bed -k 'n'
+
+
+# Create bed file corresponding to the 10kb downstream regions of the previous beds
+python3 -m src.bed_handler.bed_resize \
+  -b results/bed_file/no_readthrough_gene.bed \
+  -s 10000 \
+  -r "end" \
+  -t "outer" \
+  -o no_readthrough_gene_10kb.bed
+
+python3 -m src.bed_handler.bed_resize \
+-b results/bed_file/readthrough_gene.bed \
+-s 10000 \
+-r "end" \
+-t "outer" \
+-o readthrough_gene_10kb.bed
+
+
+exps=(all_replicates siCTRL siDDX)
+bins=(0 99)
+for exp in ${exps[*]}; do
+  for bin in ${bins[*]}; do
+    python3 -m src.visu \
+        --design data/design_exp_${exp}.txt \
+        --bw_folder data/bigwig/ \
+        --region_bed results/bed_file/readthrough_gene.bed results/bed_file/no_readthrough_gene.bed \
+        --region_name readthrough no_readthrough \
+        --output results/figures/  \
+        --border_name TSS TTS \
+        --environment 10000 25 \
+        --show_replicate n \
+        --figure_type metagene \
+        --nb_bin 100 \
+        --norm ${bin}
+
+    mv results/figures/metagene_readthrough-no_readthrough_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/${exp}_metagene_readthrough-no_readthrough_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf
+  done
+done
+
+
+exps=(all_replicates siCTRL siDDX)
+bins=(0 99)
+loc=(TSS TTS)
+for exp in ${exps[*]}; do
+  for i in ${!bins[@]}; do
+    python3 -m src.visu \
+        --design data/design_exp_${exp}.txt \
+        --bw_folder data/bigwig/ \
+        --region_bed results/bed_file/readthrough_gene_10kb.bed results/bed_file/no_readthrough_gene_10kb.bed \
+        --region_name readthrough no_readthrough \
+        --output results/figures/  \
+        --border_name TTS '' \
+        --environment 0 0 \
+        --show_replicate n \
+        --figure_type metagene \
+        --nb_bin 25 \
+        --norm "results/figures/coef_table/tmp_cov_table_design_exp_${exp}_readthrough_gene-no_readthrough_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
+
+    mv results/figures/metagene_readthrough-no_readthrough_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/${exp}_TTS10kb_metagene_readthrough-no_readthrough_25bin_0_nt-around-0-${loc[$i]}_norm.pdf
+  done
+done
+
+
+bins=(0 99)
+beds=(readthrough no_readthrough)
+for bed in ${beds[*]}; do
+  for bin in ${bins[*]}; do
+    python3 -m src.visu \
+        --design data/design_exp_all_replicates.txt \
+        --bw_folder data/bigwig/ \
+        --region_bed results/bed_file/${bed}_gene.bed \
+        --region_name ${bed} \
+        --output results/figures/  \
+        --border_name TSS TTS \
+        --environment 10000 25 \
+        --show_replicate n \
+        --figure_type metagene \
+        --nb_bin 100 \
+        --norm ${bin}
+
+    mv results/figures/metagene_${bed}_100bin_10000_nt-around-25-bin_b${bin}_norm.pdf results/figures/all_replicates_metagene_${bed}_25bin_10000_nt-around-25-bin_b${bin}_norm.pdf
+  done
+done
+
+
+beds=(readthrough no_readthrough)
+bins=(0 99)
+loc=(TSS TTS)
+for bed in ${beds[*]}; do
+  for i in ${!bins[@]}; do
+    python3 -m src.visu \
+          --design data/design_exp_all_replicates.txt \
+          --bw_folder data/bigwig/ \
+          --region_bed results/bed_file/${bed}_gene_10kb.bed \
+          --region_name ${bed} \
+          --output results/figures/  \
+          --border_name TTS '' \
+          --environment 0 0 \
+          --show_replicate n \
+          --figure_type metagene \
+          --nb_bin 25 \
+          --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${bed}_gene_100bin_10000_nt-around-25-bin_bin${bins[$i]}_norm.txt"
+
+    mv results/figures/metagene_${bed}_25bin_0_nt-around-0-bin_file_norm.pdf results/figures/metagene_TTS210kb_${bed}_25bin_0_nt-around-0-${loc[$i]}-bin_norm.pdf
+  done
+done
+
+# Graphics
+
+##############################
+#        SHY5Y               #
+##############################
+
+# Create a bed file containing
+bins=('None' 0 99)
+bin_names=('' '_b0_norm' '_b99_norm')
+for i in ${!bins[@]}; do
+  python3 -m src.visu \
+      --design data/bigwig_SHY5Y/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig_SHY5Y/ \
+      --region_bed data/bed/gene.bed \
+      --region_name all_gene \
+      --output results/figures/  \
+      --border_name TSS TTS \
+      --environment 10000 25 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin 100 \
+      --norm ${bins[$i]}
+
+  mv results/figures/metagene_all_gene_100bin_10000_nt-around-25-bin${bin_names[$i]}.pdf results/figures/metagene_5y_rnaseq_all_gene${bin_names[$i]}.pdf
+done
+
+tts_sizes=(10000 50000)
+bins=(25 125)
+for i in ${!tts_sizes[@]}; do
+  size=${tts_sizes[$i]}
+  bin=${bins[$i]}
+  kb_size=$(python -c "print(int(${size}/1000)) if ${size}/1000 == int(${size}/1000) else print(${size}/1000)")
+
+  # Create a bed file containing all gene containing one DDX-down exons
+
+  python3 -m src.bed_handler.bed_resize \
+  -b data/bed/gene.bed \
+  -s ${size} \
+  -r "end" \
+  -t "outer" \
+  -o all_gene_end${size}.bed
+
+  python3 -m src.visu \
+      --design data/bigwig_SHY5Y/design_exp_all_replicates.txt \
+      --bw_folder data/bigwig_SHY5Y/ \
+      --region_bed results/bed_file/all_gene_end${size}.bed \
+      --region_name all_gene \
+      --output results/figures/  \
+      --border_name TTS '' \
+      --environment 0 0 \
+      --show_replicate n \
+      --figure_type metagene \
+      --nb_bin ${bin} \
+      --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_gene_100bin_10000_nt-around-25-bin_bin99_norm.txt"
+
+  mv results/figures/metagene_all_gene_${bin}bin_0_nt-around-0-bin_file_norm.pdf results/figures/metagene_5y_rnaseq_TTS2${kb_size}kb_all_gene_${bin}bin_0_nt-around-0-bin_TTS_norm.pdf
+done
+
+
+# 2kb region after TSS
+
+python3 -m src.bed_handler.bed_resize \
+-b data/bed/gene.bed \
+-s 2000 \
+-r "start" \
+-o all_gene_TSS-2kb.bed
+
+
+python3 -m src.visu \
+    --design data/bigwig_SHY5Y/design_exp_all_replicates.txt \
+    --bw_folder data/bigwig_SHY5Y/ \
+    --region_bed results/bed_file/all_gene_TSS-2kb.bed \
+    --region_name all_gene \
+    --output results/figures/  \
+    --border_name TSS '' \
+    --environment 0 0 \
+    --show_replicate n \
+    --figure_type metagene \
+    --nb_bin 100 \
+    --norm "None"
+
+mv results/figures/metagene_all_gene_100bin_0_nt-around-0-bin.pdf results/figures/metagene_5y_rnaseq_TSS-2kb_all_gene.pdf