Example Data

Next Generation Sequencing example data

Import the example data into CLC Genomics Workbench:

  • Download and save the relevant data set below
  • Unless otherwise stated, unzip the file
  • Open CLC Genomics Workbench
  • Click File->Import
  • Select the appropriate NGS format to start up the appopriate Import wizard

Raw Data

Name Description Download
Illumina genomic data from Pseudomonas aeruginosa (616 MB) The data set contains four files:

  • SRR396637.sra_1.fastq and SRR396637.sra_2.fastq – paird end (FR) sequence reads. A distance range 150 to 350 is reasonable
  • SRR396636.sra_1.fastq and SRR396636.sra_2.fastq – mate pair (RF) sequence reads. A distance range 2000 to 3800 is reasonable

This data set is used in the De novo analysis of paired data tutorial

 

Illumina/Solexa paired end genome data from E. coli commensal strain K-12 (168 MB) The data set contains three files:

  • s_1_1_sequence.txt – FASTQ file containing sequence data and quality scores of the FIRST paired end reads from the E. coli K-12 genome
  • s_1_2_sequence.txt – FASTQ file containing sequence data and quality scores of the SECOND paired end reads from the E. coli K-12 genome
  • E. coli K-12 genome – A genome reference sequence of the E. coli K-12 genome is provided for read mapping.
 


CLC Formatted Data

QIAseq Panel data

Name Description Download
QIAseq TMB and MSI Panel DHS-8800Z reads This data set contains genomic sequencing reads from a tumor biopsy sample. Simply import the ZIP folder using the Standard Import tool from CLC Genomics Workbench, and analyze the reads with the Analyze QIAseq Panels guide available with the Biomedical Genomics Analysis plugin. Detail on the analysis can be found in the tutorial Compare TMB Scores and MSI Statuses from QIAseq Tumor Mutational Burden Panels.  

Mapping data

Name Description Download
CLC formatted mapping data (19.2 MB) This data set contains genomic sequencing reads from a cancer sample and a normal sample for the human mitochondrial genome. Also included is the chromosome M sequence from the hg18 build of the human genome as well as annotation tracks generated from data from UCSC Genome Browser site.
There is no need to unzip before import, simply use the Standard Import option to import the whole file. Instructions on importing this data and using it are included in the Resequencing and Tracks tutorial.
 

RNA-Seq data

Name Description Download
Subset of the full data set (12.9 MB) This data set is based on the data set published with [Mortazavi et al., 2008] and includes a subset of the full data set including a region of chromosome 16 for use as a reference.  

 

Experiments with the full data set (12.9 MB) This data set is based on the data set published with [Mortazavi et al., 2008] and includes experiments containing the expression values for the full data set.  

 

Variant and protein structure data

Name Description Download
CLC formatted variant table and molecule project (0.8 MB) This data set contains 6 variants commonly found in the Bcr-Abl fusion gene, and used in the Visualize Variants on Protein Structure tutorial.  


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