Table 1.

List of SeqCode functions.

	Name	Description	Input	Output
Custom tracks for genome browsers	buildChIPprofile	Generates a custom track from a sequencing experiment to be visualized in current genome browsers	One SAM/BAM file	The custom track in BedGraph format
	combineChIPprofiles	Generates a custom track by subtracting the second sequencing experiment from the first one to be visualized in current genome browsers	Two SAM/BAM files
Average occupancy plots	combineTSSplots	Draws the average distribution by subtracting the second sequencing experiment from the first one around the TSS of selected genes	Two SAM/BAM files, a list of genes	The average plot in PDF, the signal values and the R script
	produceGENEplots	Draws the average distribution of a sequencing experiment along the body of the meta-gene of selected genes	One SAM/BAM file, a list of genes
	producePEAKplots	Draws the average distribution of a sequencing experiment around the center of selected peaks	One SAM/BAM file, a list of BED peaks
	produceTESplots	Draws the average distribution of a sequencing experiment around the TES of selected genes	One SAM/BAM file, a list of genes
	produceTSSplots	Draws the average distribution of a sequencing experiment around the TSS of selected genes	One SAM/BAM file, a list of genes
Density heatmaps	combineTSSmaps	Draws the heatmap by subtracting the second experiment from the first one around the TSS of selected genes	Two SAM/BAM files, a list of genes	The heat map in PDF, the rank of signal values and the R script
	produceGENEmaps	Draws the heatmap of reads of an experiment along the body of the meta-gene of selected genes	One SAM/BAM file, a list of genes
	producePEAKmaps	Draws the heatmap of reads of an experiment around the centre of selected peaks	One SAM/BAM file, a list of BED peaks
	produceTESmaps	Draws the heatmap of a sequencing experiment around the TES of selected genes	One SAM/BAM file, a list of genes
	produceTSSmaps	Draws the heatmap of a sequencing experiment around the TSS of selected genes	One SAM/BAM file, a list of genes
Signal levels	recoverChIPlevels	Calculates the average, maximum, and total number of normalized reads of a sequencing experiment inside a set of regions of the genome	One SAM/BAM file, a list of regions in BED format	Average, maximum and total number of reads inside each region
Peak analysis	genomeDistribution	Distributes a list of regions of the genome into distinct gene features	A list of regions in BED format	The genome distribution in PDF, the annotation of the regions
	matchpeaks	Calculates the overlap between the components of two lists of peaks	Two lists of BED peaks	The list of overlapping peaks and the subsets of peaks that do not overlap on the other set
	matchpeaksgenes	Identifies genes genome-wide that contain one (or more) peaks from a list of selected peaks defined by the user accordingly to a set of rules and distances	A list of BED peaks	The list of genes in the genome that are target of the peaks
Evolutionary conservation	scorePhastCons	Calculates the average, maximum value, and total PhastCons score inside a set of genomic regions	A list of regions in BED format	Average, maximum and total score inside each region