Ion AmpliSeq™ Custom panels: DNA gene design input specifications
Use the following guidelines for uploading targets for Ion AmpliSeq™ Custom DNA gene designs.
Note: Although the following guidelines and examples are specific to human, the principles apply to all genome types.
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Gene symbols follow the HUGO nomenclature. The HGNC standard for human gene symbols is in ALL CAPS.
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Genomic regions are represented as number pairs (start base, end base) using the human reference genome build 19 (hg19). The system of genomic coordinates used in all Ion AmpliSeq™ inputs follows the convention of "0‑based start, 1 based end" also known as "Zero-based, half-open". For example, in a zero based system the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases that are numbered 0-99. Similarly, the region comprising the second 100 bases would be represented as (100, 200). For more information on this system of coordinates, visit http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms.
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Ion AmpliSeq™ Designer does not support designing primers for mitochondria targets. Designs for any coordinates on “chrM” will be rejected. If the mitochondrial DNA sequence is submitted for a custom reference design, the design will proceed. However, we recommend an accompanying list of polymorphisms to avoid at primer binding sites. We strongly recommend not mixing mitochondrial amplicons with those of nuclear DNA.
The following input files are accepted for Ion AmpliSeq™ Custom DNA gene designs. To view example files, in the target addition pane, click Input Specifications, then click Download this example for each file type of interest. You can copy/edit the example files to create panel‑specific input files.
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File type |
Description |
|---|---|
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Gene List |
A TXT file that contains a list of gene symbols. A Gene List TXT file is similar to a CSV file, but contains only one column. |
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CSV File |
A comma separated values (CSV) file that contains multiple columns. Column 1 specifies the type of target, such as genomic regions (REGION), CSD only (GENE_CSD), or CDS+UTRs (GENE_EXONS). Example CSV File contents, where each column is separated by a comma: |
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Amplicon ID List |
A TXT file that contains a list of amplicon IDs. The file can have a single column or multiple columns. The first column must be preceded by a header with the text "Amplicon ID". |
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BED File |
A BED file is a tab-delimited format file, with one line per feature. Required fields are chrom, chromStart, and chrmEnd in the first three columns of each file. Additional fields such as accession id, score, and strand are optional. For more information on BED files, visit http://genome.ucsc.edu/FAQ/FAQformat.html#format1. |