Clean everything prior to publication

RunSlurmExample.sh

@@ -17,23 +17,23 @@ YOUR_EMAIL=christophe.becavin@pasteur.fr
 echo $nbarray
 
 # run Mapping
-sbatch --array=${array} $folderScript/RunMapping.sh $folder/ExpDesign/${project}_List.txt
+sbatch --array=${array} $folderScript/RunMapping.sh $folder/example/${project}_List.txt
 
 # seq depth for creating Seqdepth/STAR_nbReads.txt
-sbatch --array=${array} $folderScript/RunSeqDepth.sh $folder/ExpDesign/RenameData.txt
+sbatch --array=${array} $folderScript/RunSeqDepth.sh $folder/example/RenameData.txt
 
 # count number of reads per windows, and calculate median coverage for POI
-sbatch --array=${array} $folderScript/RunWindowCovRPMF.sh $folder/ExpDesign/List.txt
-sbatch --array=${array} $folderScript/RunWindowCovPOI.sh $folder/ExpDesign/List.txt
+sbatch --array=${array} $folderScript/RunWindowCovRPMF.sh $folder/example/${project}_List.txt
+sbatch --array=${array} $folderScript/RunWindowCovPOI.sh $folder/example/${project}_List.txt
 
 # create median wig for Searching max courage
 sbatch $folderScript/RunMeanBigWig.sh $project all
 
 # Run Peak detection for every dataset
-sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/ExpDesign/${project}_exp_design.txt MACS2
-sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/ExpDesign/${project}_exp_design.txt POI
-sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/ExpDesign/${project}_exp_design.txt RPMF
-sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/ExpDesign/${project}_exp_design.txt Fisher
+sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/example/${project}_exp_design.txt MACS2
+sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/example/${project}_exp_design.txt POI
+sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/example/${project}_exp_design.txt RPMF
+sbatch --array=${array} $folderScript/RunPeakDetection.sh $folder/example/${project}_exp_design.txt Fisher
 
 # Finalize peaks detection : filter by peak occurence and regroup with bedtools
 sbatch $folderScript/RunFinalize.sh $project POI
@@ -59,7 +59,7 @@ sbatch $folderScript/RunSearchMax.sh $project Fisher $bed_name
  # final_bedfile = PATH_PEAKS + exp_design_name + '_' + peak_technique + ‘_MaxValues.bed’
 
 # Regroup peaks from different techniques
-min_number_technique=1
+min_number_technique=3
 bed_name=Raw
 sbatch $folderScript/RunRegroup.sh $project $bed_name $min_number_technique
 sbatch $folderScript/RunAnnotation.sh $project All ${bed_name}_$min_number_technique
@@ -67,31 +67,25 @@ bed_name=MaxValues
 sbatch $folderScript/RunRegroup.sh $project $bed_name $min_number_technique
 sbatch $folderScript/RunAnnotation.sh $project All ${bed_name}_$min_number_technique
 
-###### ADDED By Christophe
+# Search for max coverage center of he peak
 bed_name_max=${bed_name}_${min_number_technique}
 sbatch $folderScript/RunSearchMax.sh $project All $bed_name_max
 
-
 #Run HTSeq for peaks
+bed_name=MaxMaxValues
 bed_name_peak=${bed_name}_$min_number_technique
-array=1-102
-sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $folder/ExpDesign/${project}_List.txt $project $bed_name_peak
-bed_name=MaxValues
-sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $folder/ExpDesign/${project}_List.txt $project $bed_name_peak
+sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $folder/example/${project}_List.txt $project $bed_name_peak
 
 # Run differential analysis
-project=LiverZTall
-bed_name=Raw_1
-sbatch $folderScript/RunDiffMeth.sh $project $bed_name
-bed_name=MaxValues_3
+bed_name=MaxMaxValues_3
 sbatch $folderScript/RunDiffMeth.sh $project $bed_name
 
 # Run Salmon Analysis
-sbatch --array=${array} $folderScript/RunSalmon.sh $folder/ExpDesign/${project}_List.txt
+sbatch --array=${array} $folderScript/RunSalmon.sh $folder/example/${project}_List.txt
 sbatch $folderScript/RunSalmonAnalysis.sh ${project}
 
 # Run Motif search and Fimo
-sbatch --array=1-108 RunMotif.sh ExpDesign/Motif.txt
+sbatch --array=1-108 RunMotif.sh $folder/example/${project}_Motif.txt
 echo "Regroup motifs"
 python $folder/MeRIPSeq/src/python/motif/parse_motif_search.py -p $folder -e $project_name -b $bed_name_regroup_max
 
@@ -113,7 +107,7 @@ echo "Create motif figure with all motifs classified"
 python $folder/MeRIPSeq/src/python/motif/regroup_figures_motif.py -p $folder -e $project_name -b $bed_name_regroup_max
 
 # run Guitarplot and motif search
-sbatch --array=1-117 $folderScript/RunGuitarPlot.sh ExpDesign/GuitarPlot.txt
+sbatch --array=1-117 $folderScript/RunGuitarPlot.sh $project/example/${project}_GuitarPlot.txt
 
 # Run Venn diagram for Liver vs Cecum comparison
 Rscript $folder/MeRIPSeq/src/R/venns.R

example/Liver_List.txt

+Am_ZT3_IP_1
Am_ZT13_IP_1
CONV_ZT3_IP_1
CONV_ZT13_IP_1
Am_ZT3_Input_1
Am_ZT13_Input_1
CONV_ZT3_Input_1
CONV_ZT13_Input_1
\ No newline at end of file