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