Ion AmpliSeq™ Custom panel files

<panel ID>_ amplicon_ insert_size_ histogram.png

A PNG image of a histogram that represents the distribution of amplicon insert sizes, excluding undigested forward and reverse primer sequences and barcode adapters.

<panel ID>_ amplicon_ size_ histogram.png

A PNG image of a histogram that represents the distribution of amplicon sizes, including undigested forward and reverse primer sequences and barcode adapters.

<panel ID>_ coverage_ details.csv

A CSV file that contains exon-level coverage details, including target gene, number of amplicons that are required to cover the exon, and number of bases covered by the amplicons.

<panel ID>_ coverage_ summary.csv

A CSV file that contains gene-level coverage summary, including the total number of amplicons required to cover the CDS region of the gene and total number of bases covered by the amplicons.

<panel ID>_ Designed.bed

A BED file that defines genomic coordinates that are targeted by the primers.

<panel ID>_ Submitted.bed

A BED file that contains genomic coordinates the primers are designed to target.

<panel ID>_ Missed.bed

A BED file that contains the regions that were missed by your design. The data in this file appears as the MissedBases_AmpliSeqID_<panel ID> track that is shown in red when you link directly to the UCSC Genome Browser to review your results.

<panel ID>_ 384WellPlateDataSheet.csv

A CSV file that contains the data for your 384‑well plate. The first column contains pool information and the plate ID of your panel. The second and third columns contain the coordinates within the 384‑well plate, where each amplicon is located. Additionally, the file contains the Amplicon ID, the gene symbol, amplicon genomic coordinates (or the genomic region's coordinates), and start and stop genomic coordinates of the insert for each amplicon in the panel.

<panel ID>_DataSheet.csv (RNA designs only)

This file contains one row for each of the RefSeq accession numbers of the RNA sequences that are covered by the designed primers. For each row, there is extensive information such as the names submitted by the user, the corresponding HGNC approved symbol, the amplicon ID, the sequence of the forward and reverse primers, the start and end coordinates of the primers relative to the RefSeq sequence, the coordinates of the start and end of the amplicon, the start and end of the insert sequence relative to their position in the chromosome, and the strand of the chromosome in which the sequence is located. The last two columns of this file reports the preferred TaqMan™ assay that can be used for verification of the particular target and a classification of the of the TaqMan™ assay with 2 possible values:

• Classification 1: The recommended TaqMan™ Gene Expression Assay targets the same exon or exon-exon boundary as the Ion AmpliSeq™ RNA Design.

• Classification 2: The recommended TaqMan™ Gene Expression Assay targets the same set of RefSeq Accessions as the Ion AmpliSeq™ RNA Design.

For instructions on how to get the corresponding TaqMan™ assay, see Get TaqMan assays.

<panel ID>_Primer.bed

This file provides similar but more detailed information than the file <panel ID>_Designed.bed . There are differences in the format of some columns and in the number of rows. The differences in format make this file compatible with the UCSC Genome Browser. This file presents two rows for each one of the targets submitted to a design: one row for the forward primer and one row for the reverse primer. The start and end coordinates are the position of the primer in the chromosome that is displayed in column 1. The gene symbol in the last column corresponds to the symbol submitted by the user (it might or might not be the HGNC symbol).

plan.json

A JSON file that contains information to automatically configure a run plan for a panel in Torrent Suite™ Software.