--- a
+++ b/mermaidPlot/mermaidPlot.md
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+{
+  "theme": "default",
+  "themeVariables": {
+    "fontSize": "18px",
+    "edgeLabelBackground": "#ffffff"
+  }
+}
+
+```mermaid
+flowchart TD;
+classDef default stroke-width: 2px ;
+classDef qc fill: #ffffff ;
+	A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
+	A -->|Trimmomatic| B("Trim (.fastq.gz)")
+	B -->|Fastqc| a
+	B -->|STAR| C("Map (.bam)")
+	C -->|RseQC| c{{"Infer experiment"}}
+	C -->|featureCount| D("Count (.txt)")
+	D --> E("Downstream analysis")
+class a,c qc
+```
+
+```mermaid
+flowchart TD;
+classDef default stroke-width: 2px ;
+classDef qc fill: #ffffff ;
+	A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
+	A -->|Trimmomatic| B("Trim (.fastq.gz)")
+	B -->|Fastqc| a
+	B -->|Bowtie2| C("Map (.sam)")
+	C -->|Samtools| D("Sort (.bam)")
+	D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
+	E -->|Samtools + egrep| F("Filter (.bam)")
+	F -->|Picard: CollectInsertSizeMetrics| f{{"Insert size"}}
+	F -->|bedtools| G("Shift (.bed)")
+	F -->|Samtools: index + deepTools: bamCoverage| J("Track (.bw)")
+	subgraph H [Call peak for every sample]
+	a1("a rep_1\n(.nPeak)")
+	a2("a rep_2\n(.nPeak)")
+	an("...")
+	b1("b rep_1\n(.nPeak)")
+	b2("b rep_2\n(.nPeak)")
+	bn("...")
+	nn("...")
+	end
+	subgraph I [Call peak for grouped sample]
+		subgraph Ia [a]
+		Ia_1("a rep_1")
+		Ia_2("a rep_2")
+		Ia_n("...")
+		an("...")
+		end
+		Ia --> Ia_res1("(.nPeak)")
+		Ia --> Ia_res2("(.bdg)")
+		subgraph Ib [b]
+		Ib_1("b rep_1")
+		Ib_2("b rep_2")
+		Ib_n("...")
+		an("...")
+		end
+		Ib --> Ib_res1("(.nPeak)")
+		Ib --> Ib_res2("(.bdg)")
+		In("...")
+	end
+	G -->|MACS2| H
+	G -->|MACS2| I
+	subgraph K [Consensus peakset]
+	Ka("a (.nPeak)")
+	Kb("b (.nPeak)")
+	Kn("...")
+	end
+	I -->|IDR| K
+    H -->|IDR| K
+	I -->|bedGraphToBigWig| L("Track (.bw)")
+	K --> M("Downstream analysis")
+class a,f,Ia,Ib qc
+```
+
+```mermaid
+flowchart TD;
+classDef default stroke-width: 2px ;
+classDef qc fill: #ffffff ;
+	A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
+	A -->|Trimmomatic| B("Trim (.fastq.gz)")
+	B -->|Fastqc| a
+	B -->|Bowtie2| C("Map (.sam)")
+	C -->|Samtools| D("Sort (.bam)")
+	D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
+	E -->|Samtools + egrep| F("Filter (.bam)")
+	F -->|Picard: CollectInsertSizeMetrics| f{{"Insert size"}}
+	F -->|bedtools| G("Shift (.bed)")
+	F -->|Samtools: index + deepTools: bamCoverage| J("Track (.bw)")
+	subgraph H [Call peak for every sample]
+	Ha_1("rep_1\n(.nPeak)")
+	Ha_2("rep_2\n(.nPeak)")
+	Ha_n("...")
+	end
+	subgraph I [Call peak for grouped sample]
+		subgraph Ia [group]
+		Ia_1("rep_1")
+		Ia_2("rep_2")
+		Ia_n("...")
+		end
+		Ia --> Ia_res1("(.nPeak)")
+		Ia --> Ia_res2("(.bdg)")
+		
+	end
+	G -->|MACS2| H
+	G -->|MACS2| I
+	I -->|IDR| K("Consensus peakset (.nPeak)")
+    H -->|IDR| K
+	I -->|bedGraphToBigWig| L("Track (.bw)")
+	K --> M("Downstream analysis")
+class a,f,Ia qc
+```
+
+```mermaid
+flowchart TD;
+classDef default stroke-width: 2px ;
+classDef qc fill: #ffffff ;
+	A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
+	A -->|Trimmomatic| B("Trim (.fastq.gz)")
+	B -->|Fastqc| a
+	B -->|Bowtie2| C("Map (.sam)")
+	C -->|Samtools| D("Sort (.bam)")
+	D -->|Picard: MarkDuplicates| E("Deduplication (.bam)")
+	E -->|Samtools + egrep| F("Filter (.bam)")
+	F -->|deepTools: plotFingerprint| f{{"Coverage"}}
+	F -->|MACS2| G("Call peak (.bPeak)")
+	F -->|Samtools: index + deepTools: bamCompare| H("Track (.bw)")
+	G --> I("Downstream analysis") 
+class a,f qc
+```
+
+```mermaid
+flowchart TD;
+classDef default stroke-width: 2px ;
+classDef qc fill: #ffffff ;
+	A("Raw data (.fastq.gz)") -->|Fastqc| a{{"Quality Control"}}
+	A -->|Bismark| B("Map (.bam)")
+	B -->|Bismark: deduplicate_bismark| C("Deduplication (.bam)")
+	C -->|Bismark: bismark_methylation_extractor| D("Report CG (.txt)")
+	subgraph E [lambda]
+	E1("Map (.bam)") --> E2("Deduplication (.bam)") --> E3("Report CG (.txt)")
+	end
+	A -->|Bismark| E
+	E --> F("Filter (.txt)")
+	D --> F
+	F -->|awk| G("Arrange (.bdg)")
+	G --> H("Downstream analysis")
+	G -->|sort + bedGraphToBigWig| I("Track (.bw)")
+class a qc
+```
+