From c3620eaa38b2a9001bdb0709f3802c1f4e8c8b59 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 15 Oct 2021 14:19:49 +0200
Subject: [PATCH] src/commands.sh: update
---
src/commands.sh | 50 ++++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 49 insertions(+), 1 deletion(-)
diff --git a/src/commands.sh b/src/commands.sh
index e38aac4..3462df0 100644
--- a/src/commands.sh
+++ b/src/commands.sh
@@ -779,6 +779,7 @@ mv results/figures/metagene_all_gene_100bin_0_nt-around-0-bin.pdf results/figure
#####################################################
# Metagene figure of last exons in readthrough genes near (<=2000 nt) or far (> 2000nt) from a CTCF file and last exons from non readthrough genes
+# figures 5C
#####################################################
# Bed file containing the last exons of expressed gene with readthrough
@@ -834,4 +835,51 @@ for i in ${!list_names[*]}; do
mv results/figures/metagene_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metaexon_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf
done
-python3 -m src.gc_content -B results/bed_file/readthrough_last_exon_near_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/readthrough_last_exon_far_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/no_readthrough_expressed_last_exon.bed -b readthrough_ctcf readthrough no_readthrough -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 2000
\ No newline at end of file
+
+###########################################################
+# Figures siPP vs siCTRL pour ddx_down_ctcf,
+# , ddx_down figure 5B
+###########################################################
+
+
+list_names=(ddx_down_ctcf ddx_down)
+bed_names=(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 ${cname} \
+ --output results/figures/ \
+ --border_name " " " " \
+ --environment 10000 25 \
+ --show_replicate n \
+ --figure_type metagene \
+ --nb_bin 30 \
+ -y 0.15 0.4 \
+ --norm "results/figures/coef_table/tmp_cov_table_design_exp_all_replicates_${nbed}_100bin_10000_nt-around-25-bin_bin0_norm.txt"
+
+ mv results/figures/metagene_${cname}_30bin_10000_nt-around-25-bin_file_norm.pdf results/figures/all_replicates_metagene_${cname}_100bin_10000_nt-around-25-bin_file_norm.pdf
+done
+
+python3 -m src.gc_content -B results/bed_file/readthrough_last_exon_near_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/readthrough_last_exon_far_CTCF_2000_both_ddx_with0_exon.bed results/bed_file/no_readthrough_expressed_last_exon.bed -b readthrough_ctcf readthrough no_readthrough -g data/Homo_sapiens.GRCh37.dna.primary_assembly.fa -f "exons" -e 2000
+
--
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