Commit 9e1eddaa authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

add cut&run/tag in readme

parent 04d21226
......@@ -12,7 +12,7 @@
# What is ePeak ?
ePeak is a snakemake-based workflow for the analysis of ChIP-seq data from raw FASTQ files to differential analysis of transcription factor binding or histone modification marking. It streamlines critical steps like the quality assessment of the immunoprecipitation using the cross correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ePeak provides linear and non linear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed differences (see [chipflowr](https://gitlab.pasteur.fr/hub/chipflowr)).
ePeak is a snakemake-based workflow for the analysis of ChIP-seq/CUT&RUN/CUT&Tag data from raw FASTQ files to differential analysis of transcription factor binding or histone modification marking. It streamlines critical steps like the quality assessment of the immunoprecipitation using the cross correlation and the replicate comparison for both narrow and broad peaks. For the differential analysis ePeak provides linear and non linear methods for normalisation between samples as well as conservative and stringent models for estimating the variance and testing the significance of the observed differences (see [chipflowr](https://gitlab.pasteur.fr/hub/chipflowr)).
<img src="images/epeak_workflow.svg" width="700">
......@@ -306,9 +306,9 @@ intersectionApproach:
```
### Default mode for cut&run
### Default mode for CUT&RUN/CUT&Tag
With cut&run data, make deduplication only on INPUT/IgG data (dedup_IP to False). Then perform a stringent peak calling with SEACR and use Intersection Approach. Overlapping parameter of IA on peaks is set at 0.8.
With CUT&RUN/CUT&Tag data, make deduplication only on INPUT/IgG data (dedup_IP to False). Then perform a stringent peak calling with SEACR and use Intersection Approach. Overlapping parameter of IA on peaks is set at 0.8.
```
mark_duplicates:
......
#########################################################################
# 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:
input:
bam = compute_frip_bam,
bed = compute_frip_peaks
output:
compute_frip_csv
params:
paired = compute_frip_paired
singularity:
"epeak.img"
log:
out = compute_frip_log
shell:
"""
temp_file=$(mktemp)
if [[ {params.paired} == "True" ]]
then
#write reads as bedpe bed file to get fragments instead of reads
bedtools bamtobed -bedpe -i {input.bam} > $temp_file
else
bedtools bamtobed -i {input.bam} > $temp_file
fi
#compute number of fragments overlap peaks
mapReads=$(bedtools intersect -a $temp_file -b {input.bed} -wa -u | wc -l)
#compute number of mapped reads
totReads=$(samtools view -c -F 260 {input.bam})
#compute FRiP
totReads/mapReads
# plot_type: 'generalstats'
Sample FRiP
H3K27ac_shCtrl 1.06
H3K27ac_shUbc9 1.14
Klf4_shCtrl 1.34
Klf4_shUbc9 1.19
"""
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