Prof. Dr. Benedikt Brors, Dr. Karsten Rippe, Dr. Jan-Philipp Mallm (HD-HuB)
27.09.2017 – 29.09.2017
Institute for Pharmacy and Molecular Biotechnology (IPMB)
Im Neuenheimer Feld 364
The workshop is aimed on analyzing and interpreting RNA-seq, WGBS and ATAC-seq data. This is achieved by a practical course with introductory seminars on the computational methods used. It will teach a hands-on workflow for the analysis of sequencing data based on a rich multi-readout data set that allows it to address how DNA methylation, enhancer activity and transcription are correlated. A short introduction to basic computer skills (R, command line, etc.) needed in the course will be taught during the first day. Various analysis approaches are applied in the context of reaching the learning goals in use workflows in R and Bioconductor. Sequence read mapping will also be covered in this part. Tools used for interpretation and visualization will be introduced, these include software for the identification and integrative analysis of differential gene expression as well as of epigenetic regulation of gene expression by differential methylation of CpG islands. Furthermore, the analysis of the open chromatin landscape from ATAC-seq data will be covered. The bioinformatical analysis taught in the course will serve as the foundation and starting point for developing integrative systems models that describe the function of epigenetic networks and effects that occur in response to treatment with epigenetic drugs that target chromatin modifiers.
The course will teach background knowledge on technologies used for data generation, analysis, visualization and interpretation of RNASeq, ATAC-seq and Bisulfite sequencing data. Commonly used tools for data interpretation will be presented and can be used in hands-on parts on provided data sets.
The course is targeted at researchers who generate and/or analyze large data sets on RNASeq, ATAC-seq or bisulfite sequencing, preferentially in the context of cancer reserch. Basic knowledge in command line skills and R are highly recommended but not mandatory. A short introduction to basic computer skills (R, Linux command line, etc.) needed in the course will be taught during the first day.
Next-generation sequencing, cancer research, RNASeq, whole genome bisulfite sequencing, methylome, ATAC-seq
IGV, samtools, bedtools, DESeq2, methylCtools