- The builder spaces primer binding sites by a maximum of 150 bp whenever possible, to enable efficient enrichment of FFPE and cfDNA samples.
- When you specify gene symbols, the builder adds 5 bp of flanking intronic region around each coding exon to the target region.
- The builder archives all of your custom panels for easy reordering or retrieval of panel specifications.
- The builder uses GRCh37 as the reference genome.
The custom panel builder can be used to create:
- Custom panels – input your own content, such as genes or genomic coordinates, to build a custom panel
- Extended panels – add up to 100 primers to any cataloged panel to extend its content
- Booster panels – design a spike-in panel to either extend the content of a custom panel, or boost coverage across specific genomic regions of any panel
The custom panel builder outputs several BED files:
- Primers-150 bp: shows the expected coverage from 150 bp fragments
- Primers-250 bp: shows the expected coverage from 250 bp fragments
- ROI: region-of-interest
- ROI-not-covered-150 bp: shows genomic regions of ROI not covered based on 150 bp fragments
- ROI-not-covered-250 bp: shows genomic regions of ROI not covered based on 250 bp fragments
The reason there are two bed files is that from each primer, the protocol produces fragments of lengths between about 20 bp and 1,000 bp. The distribution of fragment lengths depends on sample quality. The 150 and 250 bp BED tracks are just illustrative. For poor sample qualities, the protocol will produce more 150 bp than 250 bp fragments. For fresh, undamaged samples, the protocol produces a lot of fragments 250 bp and up. The peak of the distribution is often around 175 bp, but the distribution peak depends highly on sample quality.