Job offer: Bioinformatician / Data scientist (f/d/m)
Modular workflows for cell annotation and pseudotime analysis of scRNA seq data
We developed a first set of diverse workflows as modular extensions of single-cell RNA-seq analysis performed with the ‘scrnaseq’ workflow. That means, all scripts use the output of ‘scrnaseq’ and perform additional analyses such as cluster annotation with reference datasets or pseudotime analysis via Monocle3 upon it. The results are returned as user-friendly html report.
Example report - Cell annotation
Example report - Pseudotime
The preprint presenting the ‘Wochenende’ pipeline developed in the RCUG is online:
‘Wochenende’ is a whole genome/metagenome sequencing alignment pipeline that works on short reads (e.g. Illumina) as well as long reads (e.g. Oxford Nanopore) and incorporates flexible quality control, trimming, mapping, various filters, and normalization. The pipeline is available on Github https://github.com/MHH-RCUG/Wochenende.
For metagenomics analysis, further modules provide a novel normalization approach for calculation of absolute abundance profiles, allow genomic visualization, integration of the pipeline results of multiple samples and their visualization.
The prerelease of ‘scrnaseq’ has been implemented by the RCUG
Single cell RNA sequencing (scRNA-seq) data analysis is an important but challenging task for users with limited knowledge in bioinformatics. To support our users, we implemented ‘scrnaseq’, a bioinformatics analysis workflow for scRNA-seq analysis developed by Dresden-concept Genome Center (TU Dresden) in close cooperation with us.
The workflow is based on Seurat and performs all substantial steps of scRNA-seq quality control, data pre-processing, including filtering, normalization and scaling, as well as data analysis, including cell clustering, differential gene expression analysis, and gene enrichment analysis.
The workflow generates a report in html format, and contains several visualizations, tables, and extensive documentation. The underlying script is currently under further revision in collaboration between the Dresden-concept Genome Center (TU Dresden) and the RCUG and you are welcome to address us if this approach is of interest for you. The first stable release is coming soon.
Client satisfaction survey of RCU Genomics services in 2020
133 working groups for which the RCU Genomics processed inquiries in 2020 were asked to vote. 109 working groups (82%) took part in the survey, of which 107 working groups (98%) judged the performance of the RCUG to be good or very good.
Job offer: Experienced specialist in Next Generation Sequencing data analysis (f/d/m)
RCU Genomics in the MHH-Info July/August 2019
This issue of the MHH-Info reports on the new technique of single-cell RNA sequencing.
Every cell counts
To date, 147 research groups at the MHH have used the services of the RCU Genomics or its predecessors
Since the formation of the microarray laboratory at the MHH (in 2001), 147 working groups from 50 departments have used the services of the RCU Genomics or the predecessor institutions.
RCUG user list (intranet)
Establishment of single-cell RNA sequencing
Joint operation of a Chromium™ Single Cell Controller from 10x Genomics by the central research institutes cell sorting and genomics.
Application approval for the Omics elective module
As part of the funding program "Quality plus - program for the development of tomorrow's studies" by the Lower Saxony Ministry for Science and Culture, our application was successfully approved for the project: Biostatistics in the age of omics technologies and big data - establishment of an elective module for the master's courses in biochemistry and biomedicine to learn analysis and evaluation of large-scale omics experiments.
Besides the RCU Genomics, the RCUs Proteomics and Metabolomics, the Institute for Clinical Biochemistry (Glycomics), the Biometry institute, and the coordinators of the two master courses were involved in the application. The new module will be developed as joined operation of these partners and will be offered to students for the first time in spring 2019.