diff --git a/TO_DO.txt b/TO_DO.txt
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+To do ?
+
+ - Differential analysis annotation is in commentary -- need to fix the issue :
+ annotation script is not working see first lines of the /pasteur/zeus/projets/p01/BioIT/Amina/Part4/epeak/workflow/scripts/annote_analysis_diff.sh
+
+ - Maybe see if this is usefull for genrich to do chipr / find a way to have similar metrics on peaks files to be able to compare tss_enrichment
+ -> some metrics are not rank the same so it might be interesting to look after this
+ -> also check on the metrics taken by lanceOtron if needed can take different values than those chosen (but work accurately for now)
+
+ - Real benchmarking on peak callers
+
+ - FriP score with subread featureCounts (check brouillon.txt)
+
+ - TSS enrichment score (check brouillon.txt)
diff --git a/brouillon.txt b/brouillon.txt
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+++ b/brouillon.txt
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+#########################################################################
+# ePeak: Standardize and reproducible ATAC-seq analysis from raw #
+# data to differential analysis #
+# Authors: Amina Alioua #
+# Copyright (c) 2024 Institut Pasteur (Paris) and CNRS. #
+# #
+# This file is part of ePeak workflow. #
+# #
+# ePeak is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# ePeak is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details . #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with ePeak (LICENSE). #
+# If not, see <https://www.gnu.org/licenses/>. #
+#########################################################################
+
+
+
+rule frip_score:
+ input:
+ frip_input_peaks
+ log:
+ out = frip_log_out,
+ err = frip_log_err
+ output:
+ frip_output
+ params:
+ gtf = config['tss_enrichment']['gtf_file'],
+ saf = frip_saf
+ singularity:
+ "epeak.sif"
+ shell:
+ """
+ touch {params.saf}
+
+ awk 'OFS="\t" {{print $4, $1, $2+1, $3, $6}}' {input} > {params.saf}
+
+ featureCounts -p -a {params.saf} -F SAF -o {output} {input} > {log.out} 2> {log.err}
+
+ """
+
+frip_input_peaks = expand(os.path.join(analysis_dir,"06-PeakCalling/{{CALLER}}/{{SAMPLE}}_peaks.narrowPeak"))
+frip_log_out = os.path.join(analysis_dir,"15-FRiP/{CALLER}/logs/{SAMPLE}_peaks.out")
+frip_log_err = os.path.join(analysis_dir,"15-FRiP/{CALLER}/logs/{SAMPLE}_peaks.err")
+frip_output = os.path.join(analysis_dir,"15-FRiP/{CALLER}/{SAMPLE}_peaks.scores")
+frip_saf = os.path.join(analysis_dir,"15-FRiP/{CALLER}/{SAMPLE}_peaks.saf")
+#final_output.extend(expand(frip_output, SAMPLE=ALL_IP_PC))
+
+for peak_caller in all_peak_caller.keys():
+ final_output.extend(expand(frip_output, CALLER=peak_caller, SAMPLE=ALL_IP_PC))
+
+include: os.path.join(RULES, "frip_scores.rules")
+
+#########################################################################
+# ePeak: Standardize and reproducible ATAC-seq analysis from raw #
+# data to differential analysis #
+# Authors: Amina Alioua #
+# Copyright (c) 2024 Institut Pasteur (Paris) and CNRS. #
+# #
+# This file is part of ePeak workflow. #
+# #
+# ePeak is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# ePeak is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details . #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with ePeak (LICENSE). #
+# If not, see <https://www.gnu.org/licenses/>. #
+#########################################################################
+
+
+
+rule tss_cov:
+ input:
+ coverage_input_bam
+ log:
+ out = coverage_log_out,
+ err = coverage_log_err
+ output:
+ bam_coverage_output
+ singularity:
+ "epeak.sif"
+ shell:
+ """
+ bamCoverage -b {input} -o {output} > {log.out} 2> {log.err}
+
+ """
+
+
+#########################################################################
+# ePeak: Standardize and reproducible ATAC-seq analysis from raw #
+# data to differential analysis #
+# Authors: Amina Alioua #
+# Copyright (c) 2024 Institut Pasteur (Paris) and CNRS. #
+# #
+# This file is part of ePeak workflow. #
+# #
+# ePeak is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# ePeak is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details . #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with ePeak (LICENSE). #
+# If not, see <https://www.gnu.org/licenses/>. #
+#########################################################################
+
+
+
+rule tss_matrix:
+ input:
+ cov = tss_input_bw,
+ bed = tss_input_bed
+ log:
+ out = tss_enrichment_log_out,
+ err = tss_enrichment_log_err
+ params:
+ gtf = config['tss_enrichment']['gtf_file']
+ output:
+ tss_enrichment_output
+ singularity:
+ "epeak.sif"
+ shell:
+ """
+ computeMatrix reference-point \
+ -S {input.cov} -R {input.bed} \
+ --referencePoint TSS \
+ -a 1000 -b 1000 \
+ --binSize 10 \
+ -o {output} > {log.out} 2> {log.err}
+
+ """
+
+
+#########################################################################
+# ePeak: Standardize and reproducible ATAC-seq analysis from raw #
+# data to differential analysis #
+# Authors: Amina Alioua #
+# Copyright (c) 2024 Institut Pasteur (Paris) and CNRS. #
+# #
+# This file is part of ePeak workflow. #
+# #
+# ePeak is free software: you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License as published by #
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# ePeak is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details . #
+# #
+# You should have received a copy of the GNU General Public License #
+# along with ePeak (LICENSE). #
+# If not, see <https://www.gnu.org/licenses/>. #
+#########################################################################
+
+
+
+rule tss_plot:
+ input:
+ tss_enrichment_output
+ log:
+ out = tss_plot_log_out,
+ err = tss_plot_log_err
+ output:
+ pdf = tss_plot_output
+ singularity:
+ "epeak.sif"
+ shell:
+ """
+ plotProfile -m {input} -out {output.pdf} > {log.out} 2> {log.err}
+
+ """
+
+
+In the Snakefile :
+ if config['tss_enrichment']['do']:
+
+ coverage_input_bam = "{}/{{SAMPLE}}_{{REF}}_sort{}.bam".format(biasedRegions_dir, biasedRegions)
+ coverage_log_out = os.path.join(analysis_dir,"14-TSS/coverage/logs/{SAMPLE}_{REF}_buffer.out")
+ coverage_log_err = os.path.join(analysis_dir,"14-TSS/coverage/logs/{SAMPLE}_{REF}_buffer.err")
+ bam_coverage_output = os.path.join(analysis_dir,"14-TSS/coverage/{SAMPLE}_{REF}_coverage.bw")
+ include: os.path.join(RULES, "tss_cov.rules")
+ final_output.extend(expand(bam_coverage_output,SAMPLE=samples,REF=ref))
+
+ tss_input_bw = expand(bam_coverage_output,SAMPLE=samples,REF=ref)
+ tss_input_bed = config['tss_enrichment']['gtf_file']
+ #tss_input_bed = "tss_gtf.gtf"
+ tss_enrichment_log_out = os.path.join(analysis_dir,"14-TSS/matrix/logs/{SAMPLE}_{REF}_buffer.out")
+ tss_enrichment_log_err = os.path.join(analysis_dir,"14-TSS/matrix/logs/{SAMPLE}_{REF}_buffer.err")
+ tss_enrichment_output = os.path.join(analysis_dir,"14-TSS/matrix/{SAMPLE}_{REF}_matrix.gz")
+ include: os.path.join(RULES, "tss_matrix.rules")
+ final_output.extend(expand(tss_enrichment_output,SAMPLE=samples,REF=ref))
+
+ #tss_enrichment_output = expand("14-TSS/{{SAMPLE}}_{{REF}}_matrix.gz")
+ tss_plot_log_out = os.path.join(analysis_dir,"14-TSS/profile/logs/{SAMPLE}_{REF}.out")
+ tss_plot_log_err = os.path.join(analysis_dir,"14-TSS/profile/logs/{SAMPLE}_{REF}.err")
+ tss_plot_output = os.path.join(analysis_dir,"14-TSS/profile/{SAMPLE}_{REF}.pdf")
+ include: os.path.join(RULES, "tss_plot.rules")
+ final_output.extend(expand(tss_plot_output,SAMPLE=samples,REF=ref))