Table 1 List of SeqCode functions.
From: Productive visualization of high-throughput sequencing data using the SeqCode open portable platform
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 |
