Galaxy software and parameters
Tool	Concatenate datasets tail-to-head (cat)	Default parameters
	Galaxy version 0.1.0
Tool	RNA STAR	Default parameters with the following exceptions:
	Galaxy version 2.5.2b-0	Read type: paired
		Reference genome: from history (using Ensembl FASTA and GTF referenced in text)
Tool	featureCounts	Default parameters with the following exceptions:
	Galaxy version 1.6.0.3	Gene annotation file: history (Ensembl GTF referenced in text)
		Count fragments instead of reads: enabled
		GFF gene identifier: gene_name
		Strand specificity: stranded-reverse
Tool	DESeq2	Default parameters with the following exceptions:
	Galaxy version 2.11.40.1	Factors: four levels, each a group of three biological replicates
		Output normalized counts table – true
		Output all levels vs. all levels – true
Tool	DEXSeq-Count	Default parameters with the following exceptions:
	Galaxy version 1.20.1	In 'read count' mode: strand-specific library – yes, reverse
Tool	DEXSeq	Default parameters with the following exception:
	Galaxy version 1.20.1	Visualize results? – no
Gene Ontology (GO) software and parameters
Tool	GO2MSIG	Parameters:
	web interface	Data source: NCBI gene2go
		Taxon ID – 7227
		Evidence codes: include EXP, IDA, IEP, IGI, IMP, IPI, ISS, TAS
		Propagate associations – true
		Use gene – symbol
		Repress IDs – no
		Create genesets for – [1 top-level domain only]
		Max. geneset size – 700
		Min. geneset size – 15
		Output format – gmt
		Database release – April 2015
Tool	GSEA Desktop for Windows	Default parameters with the following exceptions:
	v4.0.3	For up- and downregulated transcripts in Nab2ex3 vs. control:
	GSEA-Preranked	zip-report – true
		plot_top_x – 100
		create_svgs – true
		Collapse – No collapse
		For alternatively spliced transcripts in Nab2ex3 vs. control:
		zip-report – true
		Minimum gene set size – 5
		create_svgs – true
		Collapse – No collapse
Tool	AmiGO 2	Default parameters
	web interface