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Commit 347db374 authored by Rachel LEGENDRE's avatar Rachel LEGENDRE
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change name to chIPflow from ePeak

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COPYRIGHT
View file @ 347db374
ChIPflow - a snakemake-based workflow for the analysis of epigenomic data (ChIP-seq)
ePeak - a snakemake-based workflow for the analysis of epigenomic data (ChIP-seq, CUT&RUN, CUT&Tag)
from the raw fastq files to the differential analysis of transcription factor binding
or histone modification marking.
Copyright © 2020 Institut Pasteur (Paris) and CNRS.
------------------------------------------------------------------
Citation:
Daunesse M, Legendre R, Varet H, Pain A, Chica C. ChIPflow: from raw data to epigenomic dynamics
Daunesse M, Legendre R, Varet H, Pain A, Chica C. ePeak: from replicated chromatin profiling data to epigenomic dynamics
------------------------------------------------------------------
......@@ -20,7 +20,7 @@ The code includes contributions and input from:
-----------------------------------------------------------------
ChIPflow is free software: you can redistribute it and/or modify
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 version 3 of the License.
......
Snakefile
View file @ 347db374
#########################################################################
# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw #
# ePeak: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 Institut Pasteur (Paris) and CNRS. #
# #
# This file is part of ChIPflow workflow. #
# This file is part of ePeak workflow. #
# #
# ChIPflow is free software: you can redistribute it and/or modify #
# 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. #
# #
# ChIPflow is distributed in the hope that it will be useful, #
# 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 ChIPflow (LICENSE). #
# along with ePeak (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import pandas as pd
from fnmatch import fnmatch
from re import sub, match
......
config/config.yaml
View file @ 347db374
#########################################################################
# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw #
# ePeak: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 Institut Pasteur (Paris) and CNRS. #
# #
# This file is part of ChIPflow workflow. #
# This file is part of ePeak workflow. #
# #
# ChIPflow is free software: you can redistribute it and/or modify #
# 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. #
# #
# ChIPflow is distributed in the hope that it will be useful, #
# 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 ChIPflow (LICENSE). #
# along with ePeak (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
# ========================================================
# ChIPflow pipeline config file
# ePeak pipeline config file
#=========================================================
# path to the fastq directory
......@@ -222,7 +223,7 @@ seacr:
#===============================================================================
compute_idr:
do: no
do: yes
rank: 'signal.value'
thresh: 0.05
......@@ -239,7 +240,7 @@ compute_idr:
#===============================================================================
intersectionApproach:
do: yes
do: no
ia_overlap: 0.8
......
config/multiqc_config.yaml
View file @ 347db374
#########################################################################
# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw #
# ePeak: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 Institut Pasteur (Paris) and CNRS. #
# #
# This file is part of ChIPflow workflow. #
# This file is part of ePeak workflow. #
# #
# ChIPflow is free software: you can redistribute it and/or modify #
# 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. #
# #
# ChIPflow is distributed in the hope that it will be useful, #
# 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 ChIPflow (LICENSE). #
# along with ePeak (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
#===============================================================================
# Optimized MultiQc config file dedicated to ChIPflow workflow
# Optimized MultiQc config file dedicated to ePeak workflow
#===============================================================================
#------------------------------------------------------------------------------
......
test/config.yaml
View file @ 347db374
#########################################################################
# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw #
# ePeak: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 Institut Pasteur (Paris) and CNRS. #
# #
# This file is part of ChIPflow workflow. #
# This file is part of ePeak workflow. #
# #
# ChIPflow is free software: you can redistribute it and/or modify #
# 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. #
# #
# ChIPflow is distributed in the hope that it will be useful, #
# 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 ChIPflow (LICENSE). #
# along with ePeak (LICENSE). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
# ========================================================
# Config file for ChIPflow pipeline
# Config file for ePeak pipeline
#=========================================================
# directory where fastq are stored
......@@ -217,24 +218,36 @@ seacr:
threshold: 'stringent'
norm: 'norm'
#===============================================================================
# Compute IDR on replicates, pseudo-replicates and pooled replicates
#
# :Parameters:
#
# - rank: Which column to use to rank peaks. Options: signal.value p.value q.value columnIndex
# - thresh: Report statistics for peaks with a global idr below this value but return all peaks with an idr below --idr. Default: 0.05
# - intersectionApproach: set to yes if you want to use intersection approach with narrow peaks when replicates are not closed enough
# - do: if unchecked, this rule is ignored.
# - rank: which column to use to rank peaks. Options: signal.value, p.value, q.value, columnIndex
# - thresh: report statistics for peaks with a global idr below this value. Default: 0.05
#
#===============================================================================
compute_idr:
do: yes
rank: 'signal.value'
thresh: 0.05
intersectionApproach: no
#===============================================================================
# Compute intersection approach on replicates
#
# :Parameters:
#
# - do: if set to 'yes', will compute the intersection approach and use it
# to select reproducible peaks. (for narrow only, correspond to the default broad approach)
# - ia_overlap: percentage of overlap between the peaks to be selected (-f parameter of bedtools intersect). Default: 0.8
#
#===============================================================================
intersectionApproach:
do: no
ia_overlap: 0.8
#===============================================================================
......
workflow/rules/compute_FRiP_scores.rules deleted 100644 → 0
View file @ dc2876ab
#########################################################################
# ePeak: Standardize and reproducible ChIP-seq analysis from raw #
# data to differential analysis #
# Authors: Rachel Legendre, Maelle Daunesse #
# Copyright (c) 2019-2020 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 compute_FRiP_scores:
input:
bam = compute_FRiP_scores_input
output:
tab = compute_FRiP_scores_output
threads: 8
run:
import pysam
samfile = pysam.AlignmentFile(input.bam, "rb")
bed_files = ["peaks.bed"]
cr = countReadsPerBin.CountReadsPerBin([bam_file1, bam_file2],
bedFile=bed_files,
numberOfProcessors=threads)
reads_at_peaks = cr.run()
print reads_at_peaks
total = reads_at_peaks.sum(axis=0)
bam1 = pysam.AlignmentFile(bam_file1)
bam2 = pysam.AlignmentFile(bam_file2)
frip1 = float(total[0]) / bam1.mapped
frip2 = float(total[1]) / bam2.mapped
print frip1, frip2
with open(output.tab, 'w') as file_fp:
file_fp.write(S)
\ No newline at end of file
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