Commit 29c873a5 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
Browse files

agree config file to new rules

parent 64fbe7a1
......@@ -133,17 +133,21 @@ bowtie2_mapping:
threads: 4
#===============================================================================
# mark duplicates (picard-tools) identify PCR duplicates in BAM files
# mark duplicates (picard-tools) allows to mark PCR duplicate in BAM files
#
# :Parameters:
#
# - remove: If 'yes', duplicates are removed. If 'no', duplicates are flagged
# but are not filtered out. Default value: yes.
# - threads: number of threads
# - do: if unchecked, this rule is ignored.
# - dedup_IP: If true, only INPUT files will be deduplicated (ie duplicated reads
# are removed from output), IP files are only marked (ie duplicated
# reads are writted with appropriate flags set. If false all files
# will be deduplicated. Default value: true.
# - threads: number of threads to be used
#===============================================================================
mark_duplicates:
remove: 'yes'
do: yes
dedup_IP: 'True'
threads: 4
#===============================================================================
......@@ -240,6 +244,7 @@ differential_analysis:
#
# - do: if 'no', this rule is ignored.
# - options: any parameter recognized by Deeptools (see Deeptools manual)
#
#===============================================================================
bamCoverage:
......@@ -247,7 +252,37 @@ bamCoverage:
options: "--binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC"
threads: 4
#############################################################################
# GeneBody heatmap plot from Deeptools
# see https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html#usage-examples
#
# :Parameters:
#
# - do: if unchecked, this rule is ignored
# - regionsFileName: File name or names, in BED or GTF format, containing the regions to plot.
#
#===============================================================================
geneBody:
do: yes
regionsFileName: /path/to/genome/directory/mm10_genemodel.bed
threads: 4
#==============================================================================
# IGV_session produce XML session readable by IGV browser with coverage and
# peak files
#
# :Parameters:
#
# - do: if unchecked, this rule is ignored
# - autoScale:
# - normalize:
#==============================================================================
igv_session:
do: yes
autoScale: True
normalize: False
#===============================================================================
# MultiQC aggregates results from bioinformatics analyses across many
......
IP_NAME INPUT_NAME NB_IP NB_INPUT
K4Me3_C INPUT_C 1 1
K4Me3_C INPUT_C 2 2
K4Me3_U INPUT_U 2 2
K4Me3_U INPUT_U 2 1
K4Me3_U INPUT_U 1 2
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