Set some global variables for bisulfite QC

genome · Apr 17, 2019 · 46231ab · 46231ab
1 parent e62cfe6
commit 46231ab
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Showing 4 changed files with 48 additions and 2 deletions.
diff --git a/Bisulfite_QC_Coveragestats.sh b/Bisulfite_QC_Coveragestats.sh
@@ -144,6 +144,18 @@ BISCUIT_GENE="$setup_file/genes.bed.gz"
 BISCUIT_TOPGC_BED="$setup_file/windows100bp.gc_content.top10p.bed.gz"
 ## locations for the bottom 100bp bins in GC content
 BISCUIT_BOTGC_BED="$setup_file/windows100bp.gc_content.bot10p.bed.gz"
+### QC operations to perform ###
+export BISCUIT_QC_BASECOV=true
+export BISCUIT_QC_DUPLICATE=true
+export BISCUIT_QC_CPGCOV=true
+export BISCUIT_QC_CPGDIST=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_UNIFORMITY=true
+export BISCUIT_QC_CPGUNIF=true
+export BISCUIT_QC_BSCONV=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_MAPPING=true
+export BISCUIT_QC_BETAS=true
 
 >&2 echo "## Running BISCUIT QC script with following configuration ##"
 >&2 echo "=============="

diff --git a/Bisulfite_QC_CpGretentiondistribution.sh b/Bisulfite_QC_CpGretentiondistribution.sh
@@ -67,6 +67,18 @@ BISCUIT_GENE="$setup_file/genes.bed.gz"
 BISCUIT_TOPGC_BED="$setup_file/windows100bp.gc_content.top10p.bed.gz"
 ## locations for the bottom 100bp bins in GC content
 BISCUIT_BOTGC_BED="$setup_file/windows100bp.gc_content.bot10p.bed.gz"
+### QC operations to perform ###
+export BISCUIT_QC_BASECOV=true
+export BISCUIT_QC_DUPLICATE=true
+export BISCUIT_QC_CPGCOV=true
+export BISCUIT_QC_CPGDIST=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_UNIFORMITY=true
+export BISCUIT_QC_CPGUNIF=true
+export BISCUIT_QC_BSCONV=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_MAPPING=true
+export BISCUIT_QC_BETAS=true
 
 >&2 echo "## Running BISCUIT QC script with following configuration ##"
 >&2 echo "=============="

diff --git a/Bisulfite_QC_bisulfiteconversion.sh b/Bisulfite_QC_bisulfiteconversion.sh
@@ -79,6 +79,18 @@ BISCUIT_GENE="$setup_file/genes.bed.gz"
 BISCUIT_TOPGC_BED="$setup_file/windows100bp.gc_content.top10p.bed.gz"
 ## locations for the bottom 100bp bins in GC content
 BISCUIT_BOTGC_BED="$setup_file/windows100bp.gc_content.bot10p.bed.gz"
+### QC operations to perform ###
+export BISCUIT_QC_BASECOV=true
+export BISCUIT_QC_DUPLICATE=true
+export BISCUIT_QC_CPGCOV=true
+export BISCUIT_QC_CPGDIST=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_UNIFORMITY=true
+export BISCUIT_QC_CPGUNIF=true
+export BISCUIT_QC_BSCONV=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_MAPPING=true
+export BISCUIT_QC_BETAS=true
 
 >&2 echo "## Running BISCUIT QC script with following configuration ##"
 >&2 echo "=============="

diff --git a/Bisulfite_QC_mappingsummary.sh b/Bisulfite_QC_mappingsummary.sh
@@ -72,8 +72,18 @@ BISCUIT_GENE="$setup_file/genes.bed.gz"
 BISCUIT_TOPGC_BED="$setup_file/windows100bp.gc_content.top10p.bed.gz"
 ## locations for the bottom 100bp bins in GC content
 BISCUIT_BOTGC_BED="$setup_file/windows100bp.gc_content.bot10p.bed.gz"
-
-
+### QC operations to perform ###
+export BISCUIT_QC_BASECOV=true
+export BISCUIT_QC_DUPLICATE=true
+export BISCUIT_QC_CPGCOV=true
+export BISCUIT_QC_CPGDIST=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_UNIFORMITY=true
+export BISCUIT_QC_CPGUNIF=true
+export BISCUIT_QC_BSCONV=true
+export BISCUIT_QC_CGICOV=true
+export BISCUIT_QC_MAPPING=true
+export BISCUIT_QC_BETAS=true
 
 >&2 echo "## Running BISCUIT QC script with following configuration ##"
 >&2 echo "=============="