Introduction

The Bioinformatics Unit at IJC provides both internal and external researchers with high-quality computational analysis services covering all project aspects related to clinical and biological data. This includes experimental design and data analysis for microarray experiments and Next Generation Sequencing, statistical consulting, data integration, interpretation and reporting, as well as software development and data management.

Services

The unit further provides training workshops on different bioinformatics related topics, such as working in a Linux environment, the use of high-performance computing (HPC) resources, the R programming language, working with containers, best practices, etc., and supervises students.

General services:

• Data analysis, including consulting on experimental design and selection of the appropriate workflow and tools, data visualizations, report generation
• Custom analyses and tailored software development
• Data management, transfer/submission from/to public repositories (GEO, SRA, EGA)
• Support for grant and project proposal writing
• Supervision of students, bioinformatics training

Genomics:

• Genotyping and variant calling from whole-exome sequencing (WES), whole genome sequencing WGS, amplicon sequencing and SNP microarrays,

Transcriptomics:

• Differential expression analysis from RNA-seq (polyA, totalRNA) and miRNA, mRNA microarrays, target prediction
• Analysis of alternative splicing from RNA-seq
• Variant calling (e.g., RNA editing) from RNAs-eq

Epigenomics:

• Analysis of 5mC and 5hmC DNA methylation by microarray (450K, EPIC, mouse), or NGS (whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS))
• Chromatin analysis by ChIP-seq, DNAse-seq, ATAC-seq

Epitranscriptomics:

• Analysis of RNA Protein binding by CLIP-seq (binding and motif prediction)