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Next-generation Sequencing Analysis
In conjunction with other members of the Center for Human and Clinical Genetics we provide analysis of next-generation sequencing (NGS) data, as well as advice. Though comprehensive in support, our experience is primarily with the Illumina Genome Analyzer and Helicos Heliscope.
We have worked with data from many applications, including:
- ChIP-seq
- DeepCAGE
- DeepSAGE
- RNA-seq
- de novo sequencing
- SNP detection
- miRNA profiling
- targeted resequencing
Analysis varies tremendously between applications and goals, though in general we use the following set-up:
In-house we use Illumina tools to generate FASTQ files. From here analysis depends on the application used:
For additional information on data analysis we suggest looking at websites such as SEQanswers. We are also active in giving the MGC course on NGS analysis. This and additional courses can also be found at our course announcements page.
Costs:
The quotation for sequencing does not automatically include data analysis since the LGTC will not do data analysis for you. We will only do the base calling and basic QC. From that point you will receive the data from us. For now you will be able to download it via a FTP server. Soon you will get it handed over on a DVD. The files you receive are FASTQ and SRF files with the sequencing data and quality values of the called bases. We will only keep your data for three months, it is your own responsibility to make back up copies of the data you receive from us.
If you want complete data analysis to be done it has to be included in your quotation. For questions about quotations or additional information please contact the LGTC.
BioInformatics members from the LGTC:
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