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Data Analysis for GeneRead Targeted Exon Enrichment Panel

New! Cloud-Based DNAseq Sequence Variant Analysis : From raw reads to sequence variants in 3 easy steps.

This cloud-based software package for GeneRead DNAseq Targeted Exon Enrichment Panels automatically performs all the steps necessary to generate a DNA sequence variant report from your NGS data. The entire workflow consists of three easy steps.

  1. Data Upload: Upload your FASTQ files into our secure cloud space where analysis takes place.
  2. Variant Analysis: After selecting a few simple parameters, data analysis begins. Depending on the size of the sequence files, analysis can take from 30 minutes to a few hours to finish. During this step, the following processes are taking place in the cloud.

5

  1. Results Download: After the analysis is finished, you will be provided a link to download a summary and detailed variant reports as well as all the intermediate results.
  2. Example of GeneRead DNAseq Results

    • Summary of Results (.txt)
      • # of Reads
      • Coverage Specificity<
      • Coverage Depth
        • 1X, 30X, 100X Coverage Depth
        • 0.1% Median Coverage Depth
      • # SNPs / MNPs
      • # Insertions / Deletions
    • Summary of Results by Gene (.txt)
      • Gene
      • # Bases for Gene
      • % of Bases Covered by Design
      • Coverage Depth
        • 1X, 30X, 100X Coverage Depth
        • 0.1% Median Coverage Depth
      • # SNPs / MNPs
      • INDEL Count
    • Variant Identification (.xls)
      • Gene
        • Name / Chromosome # (Position)
      • Mutation Information
        • Base Mutation / Mutation Type
        • Codon Change / Amino Acid Change / Variant Frequency
      • snpEff
        • Effect / Impact
      • COSMIC
        • Mutation ID

Benefits:

Ease of Use: Simply upload your data and find your gene panel. Results are automatically analyzed without sophisticated bioinformatics training.
Convenience: Cloud-based application requires no downloading or installation. Stay current with latest gene content and software updates.
Security: User account based data management and password secured account access ensure data privacy.

To obtain more detailed instructions on using this web portal, please read "GeneRead DNAseq Variant Analysis Quick-Start Guide".

Please note that the web portal only works for data generated using GeneRead DNAseq Gene Panel from Illumina and Ion Torrent PGM sequencing platforms. Currently it is only compatible with FireFox and Chrome web browsers.

Protocol: Sample Splitting for GeneRead DNAseq Gene Panels: Ion NGS Platform

Data Analysis for GeneRead Library Quantification System

The Downloadable Excel-based Analysis Templates for Library Quantification allow easy calculation of NGS library concentration from raw threshold cycle data. Simply copy and paste the Ct values into the Excel template, the library concentration and QC scores are automatically reported in seconds.

Find the right Excel template based on your sequencing platform and PCR plate format.


GeneRead DNAseq Library Quant Array

Illumina

96-well

384-well

100-Ring

Ion Torrent PGM

96-well

384-well

100-Ring

 

GeneRead Library Quant Array or Kit

Illumina

96-well

384-well

100-Ring

Ion Torrent PGM

96-well

384-well

100-Ring

GeneRead DNA QuantiMIZE array kits

96-well

384-well

100-Ring


If you are using the GeneRead DNA QuantiMIZE assay kit, please choose the array format you used to set up your reactions.

NGS System Home
DNAseq Targeted Panels
DNAseq Mix-n-Match Panels
DNAseq Custom Panels
DNAseq Panel Mastermix
GeneRead Library Quantification
Library Quantification Mastermix