Read Mapping Parameters (CLC Genomics Workbench 8.05):
	
	Ref seq: Mesculenta_305_v6 (phytozome)
	Mapping type = Also map to inter-genic regions
       	Mismatch cost = 2
       	Insertion cost = 3
       	Deletion cost = 3
       	Length fraction = 0.8
      	Similarity fraction = 0.8
       	Global alignment = No
       	Auto-detect paired distances = Yes
       	Strand specific = Both
       	Maximum number of hits for a read = 1
       	Count paired reads as two = No
       	Expression value = RPKM		
	%%Expression values used for calculations will be RPKM values. 
       	Calculate RPKM for genes without transcripts = Yes
       	Create report = Yes
       	Create fusion gene table = No
       	Create list of unmapped reads = Yes   
 

Empirical analysis of differential gene expression (CLC Genomics Workbench 8.05): 
	
	Total count filter cutoff = 5.0
       	Estimate tagwise dispersions = Yes
       	Comparisons = All pairs
       	FDR corrected = Yes
       	
DEG Filters: 	FDR value 	< 0.01
			FC (abs)	>2


Gene Ontology Analysis:
PlantGSEA:
	Default settings (Fisher, Yekuteli (FDR), 0.01)
	


Revigo:
	Small list (similarity=0.4)
	p-values
	Database: Arabidopsis thaliana
	SimRel
	Export to R.
	Plot (Size=log10_pvalue, colour=log10_pvalue, X= frequency, Y=GO Descriptions)
	
Pathway Analysis:
	PlantGSEA:
		Enriched KEGG pathways:
			default parameters
	Pathview:
		Run both KEGG view and Graphviz on DEGs with FC values for enriched pathways.