update test with new genome and new rules

test/config.yaml

@@ -52,7 +52,7 @@ tmpdir: "/tmp/"
 #===============================================================================
 
 design:
-    design_file: test/design.txt    
+    design_file: config/design.txt    
     marks: H3K27ac, Klf4
     condition: shCtrl, shUbc9
     replicates: Rep
@@ -211,23 +211,6 @@ compute_idr:
     intersectionApproach: no
     ia_overlap: 0.8
 
-#############################################################################
-# bamCoverage from Deeptools
-#  see https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
-#
-# :Parameters:
-#
-# - do: if unchecked, this rule is ignored
-# - options: options related to deeptools
-# see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
-# for more information about effective Genome Size
-
-bamCoverage:
-    do: yes
-    options: "--binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC" 
-    threads: 4
-
-
 #===============================================================================
 # Compute differential analysis
 #
@@ -253,6 +236,56 @@ differential_analysis:
     batch: NULL
     input_counting: yes
 
+
+#############################################################################
+# bamCoverage from Deeptools
+#  see https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
+#
+# :Parameters:
+#
+# - do: if 'no', this rule is ignored.
+# - options: any parameter recognized by Deeptools (see Deeptools manual)
+#
+#===============================================================================
+
+bamCoverage:
+    do: yes
+    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: genome/mm10.refGene.gtf
+    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
 #   samples into a single report.

test/design.txt

 IP_NAME	INPUT_NAME	NB_IP	NB_INPUT
-H3K27ac_shCtrl	INPUT_shCtrl	2	2
+H3K27ac_shCtrl	INPUT_shCtrl	1	1
+H3K27ac_shCtrl	INPUT_shCtrl	2	1
+H3K27ac_shUbc9	INPUT_shUbc9	1	1
 H3K27ac_shUbc9	INPUT_shUbc9	2	1
+Klf4_shCtrl	INPUT_shCtrl	1	1
 Klf4_shCtrl	INPUT_shCtrl	2	2
-Klf4_shUbc9	INPUT_shUbc9	2	1
+Klf4_shUbc9	INPUT_shUbc9	1	1
+Klf4_shUbc9	INPUT_shUbc9	2	2

test/get_GEO_data.sh

@@ -6,18 +6,21 @@
 
 
 # Download genome references
-wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.fna.gz
-gunzip GCF_000001635.26_GRCm38.p6_genomic.fna.gz
+wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz
+gunzip mm10.fa.gz
 
 
 # get blacklisted regions
 wget http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz
 gunzip mm10.blacklist.bed.gz
 
+# download bed file for GeneBody plot
+wget http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.refGene.gtf.gz
+gunzip mm10.refGene.gtf.gz
+
 # create genome directory
 mkdir genome
-mv GCF_000001635.26_GRCm38.p6_genomic.fna genome/mm10.fa
-mv mm10.blacklist.bed genome/mm10.blacklist.bed
+mv mm10.* genome/
 
 # copy config file
 cp test/config.yaml config/config.yaml