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MeRIPSeq
Commits
6cf3ddd2
Commit
6cf3ddd2
authored
5 years ago
by
Anne BITON
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Update RunSlurmExample_test.sh
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RunSlurmExample_test.sh
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6cf3ddd2
...
...
@@ -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
# Ru
n
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 g
et 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
# G
et 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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