Ion AmpliSeq™ Designer links the output designed BED file directly to the UCSC Genome Browser automatically configured with the dbSNP and RepeatMasker annotation tracks. Although this allows you to determine if the regions were filtered based on either repeat regions or SNPs under the 3' primer, the Ion AmpliSeq™ Designer also filters for other reasons. This module offers some suggestions for using other bioinformatics tools to determine the quality of the design and for research purposes.
