This chapter explains how to visualize tracks, how to retrieve reference data and finally how to perform generic comparisons between tracks.

A track is the fundamental building block for NGS analysis in the CLC Genomics Workbench. The idea behind tracks is to provide a unified framework for the visualization, comparison and analysis of genome-scale studies such as whole-genome sequencing or exome resequencing projects and a variety of different -Seq data (i.e. RNA-seq, ChIP-Seq, DNAse-Seq).24.1

In tracks, all information is tied to genomic positions. A central coordinate-system is provided by a reference genome, which allows that different types of data or results for different samples can be seen and analyzed together.

Different types of data are represented in different types of tracks, and each type of track has its own particular editors. An example of a paired-end mapping read-track displaying reads and coverage is shown in figure 24.1.

Image readtrack1
Figure 24.1: A paired-end mapping read-track opened, displaying reads and coverage. On the top right, the button for creating a Track List is visible. On the right is the SidePanel.

The different track types in the CLC Genomics Workbench are:

A sequence (Image sequence_track_16_n_p)
This is the track type that is used for holding the reference genome. The sequence track contains the single reference sequences of the genome (e.g. the chromosomes or the consensus sequences of de novo assembled contigs).
A reads track (Image read_track_16_n_p)
This is the track type that is used for holding a read mapping e.g. as produced by the Map Reads to Reference, Local Realignment or RNA-Seq Analysis tools.The reads track contains all the reads that have been mapped at their mapped positions, and you can zoom in all the way to base resolution.
A variant track (Image variant_track_16_n_p)
A variant track is a particular kind of track that is used to store features that fulfill the requirements for being a variant. A particular requirement for being a variant is that it refers to a particular region of the reference, and it is possible to describe exactly how the sample "Allele" sequence looks in this region, as compared to what the "reference allele" sequence looks like in this region.

Variants may be of type SNV, MNV, replacement, insertion or deletion. A variant track may be produced either by running a Variant detection analysis (e.g using the Probabilistic or Quality-based variant callers or by importing a variant format file (such as a "vcf" or a "gvf" file) or downloading it from a database (e.g. COSMIC or dbSNP).

The tool InDels and Structural Variants detects structural variants, including insertions, deletions, inversions, translocations and tandem duplications. It will produce a variant track, which will contain some insertions and deletions (the "InDel" track). However, the tool will also detect some insertions for which the "Allele" sequence is not fully, but only partially, known. These insertions do not fulfill the requirements of being a variant and therefore cannot be put in the variant track. Instead they are put in the "SV track", along with the inversions and translocations. The "SV" track is an "annotation" (or "feature") track, which is less strict and more flexible, in the requirements to the types of annotations (or features) that it can contain (see below).

An annotation track (Image annotation_track_16_n_p)
Each annotation track contains a certain type of annotations. Examples are gene or mRNA tracks, which contain gene, respectively mRNA, annotations, UTR tracks, conservation score tracks and target region tracks. They may be obtained either by importing (Import Tracks or downloading them into the Workbench (e.g from a .bed, .gtf or .gff file or a database, such as ENSEMBL). Also, many of the tools in the CLC Genomics Workbench will output annotation tracks. Examples are the Indels and Structural Variants tool, which will put the detected structural variants (that do not fulfill the requirements for being of type "variant") in an annotation track, or the ChIP-seq detection tool which will put the detected "peaks" into a "peak" annotation track. A description of how to annotate and filter tracks is found in Annotate and filter tracks.
A coverage graph (Image graph_track)
The coverage graph track is calculated from a reds track and contains a graphical display of the coverage at each position in the reference.
An expression track (Image rnaseqtrack_16_h_p)
The RNA-seq algorithm produces expression tracks; one for genes and one for transcripts. These are tracks that have an annotation for each gene, respectively transcript, and an expression value associated to that annotation.

An example of the different types of tracks is given in figure 24.2.

Image tracktypes
Figure 24.2: A tracklist containing different types of tracks. From the top: a sequence track, three annotation tracks with gene, mRNA and CDS annotations respectively, two variant tracks, a gene-level (GE) and a transcript level (TE) expression track, a coverage track and a reads track.

For comparison tools specific to resequencing and variants, please see Resequencing.


... DNAse-Seq).24.1
The track concept was first introduced with the Genomics Gateway plugin in 2011 and made an integral part of the CLC Genomics Workbench 5.5 release.