Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
ePeak
Manage
Activity
Members
Plan
Wiki
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Deploy
Releases
Package registry
Container Registry
Model registry
Operate
Terraform modules
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
hub
ePeak
Commits
cb96e9b2
Commit
cb96e9b2
authored
3 years ago
by
Rachel LEGENDRE
Browse files
Options
Downloads
Patches
Plain Diff
fix error in IA when nomodel
parent
732d6674
No related branches found
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
workflow/rules/compute_frip.rules
+0
-65
0 additions, 65 deletions
workflow/rules/compute_frip.rules
with
0 additions
and
65 deletions
workflow/rules/compute_frip.rules
deleted
100755 → 0
+
0
−
65
View file @
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
"""
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment