Supported species

The following species are already supported for NGS analysis, if you would like to perform analysis on a new or different species please contact us so we can arrange the addition of that species to our portfolio.

Vertebrates (DNA+RNA);

  • Human (GRCH37.74)
  • Mouse (GRCm38.70)
  • Rat (Rnor50.71)
  • Dog (CanFam31.75)
  • Pig (Sscrofa11.1.91)
  • Zebrafish (Zv9.75)

Plants (DNA+RNA);

  • Arabidopsis (TAIR10.30)
  • Tomato (ITAG3.20)

Bacteria (DNA);

  • Staphylococcus pasteuri (ASM49487v1)
  • Staphylococcus simulans (ASM155911v1)

Yeast (DNA);

  • Saccharomyces cerevisiae (R64-1-1)

 

Grant Applications

We provide a boilerplate text that describes the services provided by UBEC/UMC Utrecht in the field of data management/stewardship.

The text provided can be used for the Data Management Plan paragraph that is present in your Grant-application. Please note that the information in this document assumes the default set-up of a project within the UMC UtrechtCenter for Molecular Medicine. If your project deviates from this standard, the default text should be edited to reflect those changes. Please contact us if this is the case, so we can include it in our repository and keep track of the possible scenarios and use cases.

The text is maintained and versioned at GitHub.

 

Darrin Higgins, Noun Project, CC BY 3.0 US: https://creativecommons.org/licenses/by/3.0/us/, https://thenounproject.com/term/dna/3928/, changed black icon to white, increased canvas size

NGS analysis

We run and help maintain the Illumina Analysis Pipeline developed within the CMM.

https://github.com/UMCUGenetics/IAP

This pipeline can perform the different steps required to go from sequencing output (FASTQ) to mapped data (BAM) or called and annotated variants (VCF).

We offer the following services (*prices ex VAT):

AnalysisUnitService fee *Data type
Mapping + germline SNV/InDel callingsample€ 50DNA
CNV + SV callingsample€ 15DNA
Mapping + somatic callingtumor/normal pair€ 120DNA
Mapping + read count analysisrun€ 50mRNA
Differential expression analysis + figurescomplete set€ 50mRNA
* Service fees in euro's, excluding VAT

FAIR check

In accordance to the FAIR principles both data and analysis should be Findable, Accessible, Interoperable and Reproducible.

We provide input on how to make your research reproducible. One of the services we provide to achieve this is the FAIR check.

Prior to publication you can provide us with your draft and we will check the following items;

  • Data availability (F and A)
  • Code availability (F and A)
  • Interoperability  (I)
  • Reproducibility  (R)

Based on our assessment we can provide your draft with a FAIR rating which can be included in the cover letter and final publication.

If one of the components fails or can be improved you can work together with the UBEC to remedy this and increase your chances of publication.

 

Data Analysis

We provide analysis of clusters and patterns within high dimensional data to facilitate high quality research with the Utrecht Life Sciences community.

We ensure that all analysis are publication ready by utilising specialised plotting libraries and writing reproducible and clear code.

 

Some examples of the types of analysis one can think of are listed below:

  • Random forest classification

randomforest

  • Principal Component Analysis

PCAexample

  • Heatmaps

HeatmapExample

End to end

The UBEC provides guidance and support throughout the research track from design to publication, an end to end service.

We can provide input on the design of the experiment, plans for proper data management, produce high quality figures and upload the data and code to the appropriate resources.