Data Processing and Analysis

Primary data processing transforms raw data generated by high-throughput instruments into formats suitable for further analysis. In addition, QC reports and checksum files are created to verify the integrity of transferred data.

User fees & service usage: Free of charge, as this is included in the services of the data-generating Core Facilities at Helmholtz Munich.

We offer secondary data processing for different data types and technologies including re-processing of published datasets. The computational pipelines perform all necessary steps (e.g. QC, alignment, peak calling, feature counting etc.) required for downstream analyses. We perform quality controls and offer user consultation and support on demand.

Ready to use computational pipelines based on workflow frameworks such as Nextflow [1] and executed on a High-Performance Compute (HPC) cluster are available for the following technologies.

Computational pipelines

Bulk sequencing: 

• RNA-Seq (nf-core) & miRNA-Seq
• Assembly and identification or Immunoglobulins from RNA-Seq data (igfinder)
• ChIP-Seq (ChIP-seq, cutandrun, nf-core)
• ATAC-Seq (nf-core)
• WGS variant calling (Sarek, nf-core)
• Methyl-Seq (nf-core)
• Crispr-Seq (nf-core)

Single cell sequencing:  

• 10x Genomics workflows
• Single cell variant calling and genomic demultiplexing (vireo, monopogen)
• Parse Biosciences workflow

Long read sequencing:

• scnanoseq (nf-core)
• Parse Biosciences workflow

Illumina Genotyping Arrays:

• Karyotyping pipeline  

References

[1] https://www.nextflow.io

Further information for Helmholtz Munich users regarding the usage of the pipelines is available here.

User fees: Per project depending on the number of samples processed.

Booking: We offer data processing with our computational pipelines through Services, which can be booked via iLabs (service name: Secondary Data Analysis)

Custom data analysis refers to tailored data analysis and statistical consulting projects conducted for core facility users. These projects may range from bioinformatics to statistical consulting or combine both components. At the beginning of each project a consultation session is scheduled with the user to discuss the project scope, potential analysis strategies, milestones and expected outcomes. Once the written project proposal has been accepted, the core facility will begin implementing the project. Customers can expect updates during interim meetings and will receive both interim reports and a final report with the results. Upon completion users will also be provided with the computational methods and materials developed for the project.

User fees: Scope and costs are determined by the project proposal and the estimated hours required for implementation.

Booking: Please send us a request through iLabs (service name Custom data analysis and consulting). We will schedule an initial meeting to discuss and set up the project proposal. This meeting will be free of charge.