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Commit 6cf3ddd2 authored by Anne  BITON's avatar Anne BITON
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Update RunSlurmExample_test.sh

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......@@ -23,18 +23,15 @@ export PATH=$PATH:~/tools/WiggleTools/bin/
#module load R/3.5.0
module load R/3.4.1
#project=Cecum_all
#project=Liver_all
#project=Liver_all_T13
#project=Cecum_2019
#project=CecAm
#project=Liver_2019
#project=LiverZT
#project=Liver_2019_T13
#project=Liver_2018_T13
project=Cecum_allWithoutEc
listfile=$folder/ExpDesign/${project}_List.txt #_Lp8-T3.txt
expdesign_file=$folder/ExpDesign/${project}_exp_design.txt #_Lp8-T3.txt
listfile=$folder/ExpDesign/${project}_List.txt
expdesign_file=$folder/ExpDesign/${project}_exp_design.txt
array=$(wc -l $listfile | awk '{print $1}')
array="1-"$array
echo $array
......@@ -56,27 +53,28 @@ export PATH=$PATH:~/tools/WiggleTools/bin/
module load R/3.4.1
# run Mapping
# sbatch --array=${array} $folderScript/RunMapping.sh $listfile
sbatch --array=${array} $folderScript/RunMapping.sh $listfile
# seq depth for creating Seqdepth/STAR_nbReads.txt
# sbatch --array=${array} $folderScript/RunSeqDepth.sh $folder/ExpDesign/${project}_Rename.txt
sbatch --array=${array} $folderScript/RunSeqDepth.sh $folder/ExpDesign/${project}_Rename.txt
# count number of reads per windows, and calculate median coverage for POI
# sbatch --array=${array} $folderScript/RunWindowCovRPMF.sh $listfile
# sbatch --array=${array} $folderScript/RunWindowCovPOI.sh $listfile
sbatch --array=${array} $folderScript/RunWindowCovRPMF.sh $listfile
sbatch --array=${array} $folderScript/RunWindowCovPOI.sh $listfile
# # create median wig for Searching max coverage
# sbatch $folderScript/RunMeanBigWig.sh $project all
# create median wig for Searching max coverage
sbatch $folderScript/RunMeanBigWig.sh $project all
# sbatch $folderScript/RunMeanBigWig.sh $project abx
# sbatch $folderScript/RunMeanBigWig.sh $project abx_GF
# sbatch $folderScript/RunMeanBigWig.sh $project ex_GF
# sbatch $folderScript/RunMeanBigWig.sh $project Am
# sbatch $folderScript/RunMeanBigWig.sh $project CONV
# sbatch $folderScript/RunMeanBigWig.sh $project Ec
# sbatch $folderScript/RunMeanBigWig.sh $project GF
# sbatch $folderScript/RunMeanBigWig.sh $project Lp
# sbatch $folderScript/RunMeanBigWig.sh $project vanco
# create median coverage wig file for each condition
sbatch $folderScript/RunMeanBigWig.sh $project abx
sbatch $folderScript/RunMeanBigWig.sh $project abx_GF
sbatch $folderScript/RunMeanBigWig.sh $project ex_GF
sbatch $folderScript/RunMeanBigWig.sh $project Am
sbatch $folderScript/RunMeanBigWig.sh $project CONV
sbatch $folderScript/RunMeanBigWig.sh $project Ec
sbatch $folderScript/RunMeanBigWig.sh $project GF
sbatch $folderScript/RunMeanBigWig.sh $project Lp
sbatch $folderScript/RunMeanBigWig.sh $project vanco
# sbatch $folderScript/RunMeanBigWig.sh $project Am_Liver_2018
......@@ -98,78 +96,78 @@ module load R/3.4.1
# sbatch $folderScript/RunMeanBigWig.sh $project Liver_Lp_T3
# # Ru Peak detection for every dataset
# sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file MACS2
# sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file POI
# sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file RPMF
# Run Peak detection for every dataset
sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file MACS2
sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file POI
sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file RPMF
# attention! FIsher ne marche pas si HTSeq est loade pour des histoires obscures de library
#module unload HTSeq
# sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file Fisher
module unload HTSeq
sbatch --array=${array} $folderScript/RunPeakDetection.sh $expdesign_file Fisher
# # Finalize peaks detection : filter by peak occurence and regroup with bedtools
# sbatch $folderScript/RunFinalize.sh $project POI
# sbatch $folderScript/RunFinalize.sh $project MACS2
# sbatch $folderScript/RunFinalize.sh $project RPMF
# sbatch $folderScript/RunFinalize.sh $project Fisher
sbatch $folderScript/RunFinalize.sh $project POI
sbatch $folderScript/RunFinalize.sh $project MACS2
sbatch $folderScript/RunFinalize.sh $project RPMF
sbatch $folderScript/RunFinalize.sh $project Fisher
# # for every technique ->
# # final_bedfile = PATH_PEAKS + exp_design_name + '_' + peak_technique + ‘_Raw.bed'
# # Annotate peaks, search for overlapping genes, create gif and bed file, overlap with ref peaks
# sbatch $folderScript/RunAnnotation.sh $project Fisher Raw
# sbatch $folderScript/RunAnnotation.sh $project POI Raw
# sbatch $folderScript/RunAnnotation.sh $project RPMF Raw
# sbatch $folderScript/RunAnnotation.sh $project MACS2 Raw
sbatch $folderScript/RunAnnotation.sh $project Fisher Raw
sbatch $folderScript/RunAnnotation.sh $project POI Raw
sbatch $folderScript/RunAnnotation.sh $project RPMF Raw
sbatch $folderScript/RunAnnotation.sh $project MACS2 Raw
# # final_bedfile = PATH_PEAKS + exp_design_name + '_' + peak_technique + ‘_Raw.bed’
# # Search for Max coverage = summit of the peaks
bed_name=Raw
# sbatch $folderScript/RunSearchMax.sh $project MACS2 $bed_name
# sbatch $folderScript/RunSearchMax.sh $project RPMF $bed_name
# sbatch $folderScript/RunSearchMax.sh $project POI $bed_name
# sbatch $folderScript/RunSearchMax.sh $project Fisher $bed_name
# Search for Max coverage = summit of the peaks
bed_name=Raw
sbatch $folderScript/RunSearchMax.sh $project MACS2 $bed_name
sbatch $folderScript/RunSearchMax.sh $project RPMF $bed_name
sbatch $folderScript/RunSearchMax.sh $project POI $bed_name
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=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
bed_name=MaxValues
#sbatch $folderScript/RunRegroup.sh $project $bed_name $min_number_technique
#sbatch $folderScript/RunAnnotation.sh $project All ${bed_name}_$min_number_technique
# Regroup peaks from different techniques
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
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, to get MaxMaxValues
bed_name_max=${bed_name}_${min_number_technique}
#sbatch $folderScript/RunSearchMax.sh $project All $bed_name_max
#sbatch $folderScript/RunAnnotation.sh $project All MaxMaxValues_$min_number_technique
# Get MaxMaxValues
bed_name_max=${bed_name}_${min_number_technique}
sbatch $folderScript/RunSearchMax.sh $project All $bed_name_max
sbatch $folderScript/RunAnnotation.sh $project All MaxMaxValues_$min_number_technique
# #Run HTSeq for peaks
bed_name=Raw
bed_name_peak=${bed_name}_$min_number_technique
# Run HTSeq for peaks
bed_name=Raw
bed_name_peak=${bed_name}_$min_number_technique
# array=1-64
# sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $listfile $project $bed_name_peak
bed_name=MaxValues
bed_name_peak=${bed_name}_$min_number_technique
#sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $listfile $project $bed_name_peak
bed_name=MaxMaxValues
bed_name_peak=${bed_name}_$min_number_technique
sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $listfile $project $bed_name_peak
# # Run differential analysis
bed_name=Raw
bed_name_peak=${bed_name}_$min_number_technique
#sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
bed_name=MaxValues
bed_name_peak=${bed_name}_$min_number_technique
#sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
bed_name=MaxMaxValues
bed_name_peak=${bed_name}_$min_number_technique
# sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
bed_name=MaxValues
bed_name_peak=${bed_name}_$min_number_technique
#sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $listfile $project $bed_name_peak
bed_name=MaxMaxValues
bed_name_peak=${bed_name}_$min_number_technique
sbatch --array=${array} $folderScript/RunHTSeqPeaks.sh $listfile $project $bed_name_peak
# Run differential analysis
bed_name=Raw
bed_name_peak=${bed_name}_$min_number_technique
#sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
bed_name=MaxValues
bed_name_peak=${bed_name}_$min_number_technique
#sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
bed_name=MaxMaxValues
bed_name_peak=${bed_name}_$min_number_technique
sbatch $folderScript/RunDiffMeth.sh $project $bed_name_peak
# # run Guitarplot and motif search
#sbatch --array=1-78 $folderScript/RunGuitarPlot.sh ExpDesign/Cecum_all_GuitarPlots.txt
......
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