Verified Commit 335fee38 authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

tweak gene body in metagene plots

parent a09bd0bb
......@@ -8,9 +8,6 @@ single_end: True
resources:
ref:
# Number of chromosomes to consider for calling.
# The first n entries of the FASTA will be considered.
n_chromosomes: 16
# Ensembl species name
species: saccharomyces_cerevisiae
# Ensembl release
......@@ -47,9 +44,6 @@ params:
activate: False
picard_metrics:
activate: True
deseq2:
# set to True to use the vst transformation instead of the rlog transformation for the DESeq2 analysis
vst: False
peak-annotation-analysis:
activate: True
peak-qc:
......
......@@ -135,16 +135,16 @@ rule compute_matrix:
matrix_tab="results/deeptools/matrix_files/matrix.tab"
log:
"logs/deeptools/compute_matrix.log"
threads: 2
threads: 6
params:
command="scale-regions",
extra="--regionBodyLength 1000 "
extra="--regionBodyLength 5000 "
"--beforeRegionStartLength 3000 "
"--afterRegionStartLength 3000 "
"--missingDataAsZero " # added to prevent black output in the heatmap (plot_heatmap rule) https://github.com/deeptools/deepTools/issues/793
"--skipZeros "
"--smartLabels "
"--numberOfProcessors 2 "
"--numberOfProcessors 6 "
wrapper:
"0.64.0/bio/deeptools/computematrix"
......
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