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SureDesign provides a set of BED-format track files for each custom design that you can download and view in a compatible genome browser to analyze the coverage of the design.
The tracks that are included in the downloadable BED files are described below.
For coverage analysis of your design:
· Use the Target Regions track as the list of all desired capture regions.
· Use the Covered track as the list of all capture regions capable of being sequenced.
This track is contained in the BED files [design ID]_Regions.bed and [design ID]_AllTracks.bed.
The regions in this track are the target regions for which SureDesign selected the probes for the design. You can use this track to determine how SureDesign mapped your target regions of interest (as defined in the design wizard) to specific sequences in the genome.
This track is contained in the BED files [design ID]_Covered.bed and [design ID]_AllTracks.bed.
The regions in this track are the genomic regions that are covered by one or more probes in the design. To identify these regions, SureDesign first determines the expected amplicon sequence for each probe in the design, then removes 5 bp of sequence from each end to account for artifacts caused by the sequence aligner or quantitative PCR. When you use the design for target enrichment, the genomic regions that will ultimately be sequenced depend on the read length (for Illumina design) or the flow sequence (for Ion Torrent design).
SureDesign generates an Amplicons track for HaloPlex designs only. The track is contained in the BED file [design ID]_AllTracks.bed.
This track contains the full amplicon sequences expected for all probes in the design. Unlike the Covered track, the Amplicons track includes the entire amplicon, not just the portion that can be sequenced.
This track is contained in the BED file [design ID]_AllTracks.bed.
The Missed track contains any regions from the Target Regions track that are not included in the Covered track. You can use the Missed track to view genomic regions that you are interested in sequencing but cannot sequence using that particular design.
You can view the tracks into a compatible genome browser program, such as the UCSC Genome Browser, by uploading a BED file as a custom track. See http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#ADD_CT for instructions on loading a custom track into the UCSC Genome Browser.
The image below shows the Target Regions, Covered, and Missed tracks for a HaloPlex design viewed in the UCSC Genome Browser. The browser is also displaying the RefSeq Genes track, which is a human genome track created by UCSC that depicts gene regions taken from the RefSeq collection.
See Also