Reformat and Upload a Gene List

1. Open the original TruSeq Custom Amplicon design gene list file (*.csv) in a spreadsheet editor, such as Excel.
2. Delete the following columns:
3. Rename the TargetType column into Type and move it to the left of the Gene column.
4. Enter Chromosome in the header of the column to the right of the Gene column.
5. Enter Start in the header of the column to the right of the Chromosome column.
6. Enter End in the header of the column to the right of the Start column.
7. Rename the Gene column into Name.
8. Enter GENE_CDS for all CDS entries and GENE_EXON for all Exon entries in the Type column.
9. Enter GENE_CDS or GENE_EXON for each FullRegion entry in the Type column. Alternatively, use a coordinate input file to upload FullRegion entries. See Reformat and Upload a Coordinates File.


The full target region will not be covered when using GENE_CDS or GENE_EXON for FullRegion entries.

10. The Chromosome, Start, and End columns can be empty.
11. Save and close the gene list file.
12. Create a new AmpliSeq for Illumina Gene design. See Create an AmpliSeq for Illumina Gene Design.

Make sure to select the species that matches the original TruSeq Custom Amplicon design. For human TruSeq Custom Amplicon designs, select Human (hg19).

13. Configure the new AmpliSeq for Illumina design by selecting the Sample Type and Max Amplicon Length that most closely match those of the original TruSeq Custom Amplicon design.

Use the following table for selecting equivalent amplicon sizes between the two assay types:

TruSeq Custom Amplicon design Amplicon Size

AmpliSeq for Illumina custom design Max Amplicon Size









14. Use the default setting for Stringency.
15. Select Next.
16. Upload the reformatted gene list file into the AmpliSeq for Illumina design. See Add Targets by Uploading Files.