Commit cb96e9b2 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

fix error in IA when nomodel

parent 732d6674
#########################################################################
# 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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