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Illumina HiSeq copy number data are results from Illumina HiSeq Sequencing done using low-coverage sequencing.

Data Overview

Illumina HiSeq copy number data is derived by low-pass, whole genome sequencing of the tumor and normal samples, and subsequent analysis of differences in read count representation across the genome. For this platform, Level 3 data represents the difference in coverage between the tumor and normal samples.  VCF files representing inferred translocations and deletions are anticipated.

Available Platforms

Platform Code

Platform Alias

Platform Name

Available

Example

FTP

IlluminaHiSeq_DNASeqC

IlluminaHiSeq_DNASeqC

Illumina HiSeq for Copy Number Variation

Yes

example icon

/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<disease_study>/cgcc/hms.harvard.edu/illuminahiseq_dnaseqc/cna/

Data File Formats

Level_1 data are BAM files, generated from tumor and normal samples and are not archived at DCC.

Level_3 data describes regions with differences in genome coverage (number of reads) between normal and tumor samples.

Platform Code

Data Level

File Type

Description

Example

IlluminaHiSeq_DNASeqC

Level_3

.tsv

tab delimited
Chromosome
Start
End
Tumor_Count
Normal_Count
Segment_Mean

example icon

Validation

Specific Validations

Apart from the standard GCC validation set listed below, Illumina HiSeq Copy Number has no data type-specific validations.

Standard Validations

IlluminaHiSeq_DNASeqC archives undergo standard validation sets shown in the Standard Archive Validation chart for GCC archives:

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