Skip to content
Snippets Groups Projects
Commit cb96e9b2 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

fix error in IA when nomodel

parent 732d6674
No related branches found
No related tags found
No related merge requests found
#########################################################################
# 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
"""
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment