Skip to content
Snippets Groups Projects
Select Git revision
  • f797c9eb9602c03932e8a7403a9840d90b2f8bda
  • master default protected
2 results

RunSlurmExample.sh

Blame
    • RunSlurmExample.sh 4.18 KiB
    1
    2
    3
    4
    5
    6
    7
    8
    9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27
    28
    29
    30
    31
    32
    33
    34
    35
    36
    37
    38
    39
    40
    41
    42
    43
    44
    45
    46
    47
    48
    49
    50
    51
    52
    53
    54
    55
    56
    57
    58
    59
    60
    61
    62
    63
    64
    65
    66
    67
    68
    69
    70
    71
    72
    73
    74
    75
    76
    77
    78
    79
    80
    81
    82
    83
    84
    85
    86
    87
    88
    89
    90
    91
    92
    93
    94
    95
    96 
    

    

    

    #!/bin/bash
# run the script using
# Run.sh should be executable
# chmod 777 Run.sh
# nohup ./Run.sh > Run.log 2>&1 &

folder=/pasteur/projets/policy01/m6aAkker
folderScript=$folder/MeRIPSeq/src/bash_slurm
#project=CecAm
#project=Cecum
#project=Liver
project=LiverZTall
listfile=$folder/ExpDesign/${project}_List.txt
nbarray=$(wc -l $listfile | awk '{print $1}')
echo $nbarray

# run Mapping
sbatch --array=${array} $folderScript/RunMapping.sh $folder/ExpDesign/${project}_List.txt

# seq depth for creating Seqdepth/STAR_nbReads.txt
sbatch --array=${array} $folderScript/RunSeqDepth.sh $folder/ExpDesign/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

# 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

# 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
# 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
# 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
 # final_bedfile = PATH_PEAKS + exp_design_name + '_' + peak_technique + ‘_MaxValues.bed’

# Regroup peaks from different techniques
min_number_technique=1
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
bed_name_max=${bed_name}_${min_number_technique}
sbatch $folderScript/RunSearchMax.sh $project All $bed_name_max


#Run HTSeq for peaks
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

# Run differential analysis
project=LiverZTall
bed_name=Raw_1
sbatch $folderScript/RunDiffMeth.sh $project $bed_name
bed_name=MaxValues
sbatch $folderScript/RunDiffMeth.sh $project $bed_name

# run Guitarplot and motif search
sbatch --array=1-117 RunGuitarPlot.sh ExpDesign/GuitarPlot.txt
sbatch --array=1-108 RunMotif.sh ExpDesign/Motif.txt
sbatch --array=1-8 RunMotif.sh ExpDesign/Motif2.txt

sbatch --array=1-3 MeRIPSeq/src/bash_slurm/RunFimo.sh PeakDiffExpression/CecAm_MaxMaxValues/Motif/Fimo.sh
sbatch --array=1-11 MeRIPSeq/src/bash_slurm/RunFimo.sh PeakDiffExpression/CecAm_MaxMaxValues/Motif/Centrimo.sh

#echo "Your MeRIPSeq pipeline ended "$(date "+%A %B %d at %H:%M:%S") | mailx -s "MeRIPSeq pipeline" "christophe.becavin@pasteur.fr"