The German Crop BioGreenformatics Network (GCBN) as one service unit within the German Network for Bioinformatics Infrastructure (de.NBI) presents the first HandsOn training that will be organized by the the Forschungszentrum Jülich (FZJ) and the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. The GCBN is specialized in the diversified field of Omics data analysis for crop plants.
Educators:
GCBN-FZJ: Alisandra Denton
GCBN-IPK: Thomas Schmutzer, Andrea Bräutigam
Date:
19-OCT-2016 – 21-OCT-2016
Location:
IPK Gatersleben, Bioinformatikzentrum, Room No 1.32,
Corrensstraße 3, 06466 Stadt Seeland
Contents:
The 3rd GCBN user training will focus on the workflow from a user driven perspective guided from raw sequence data to biological interests and hypothesis. During the training participants will gain insights into the use of relevant tools for transcriptomic and genomic data analysis. Major parts are compiled as HandsOn training completed with lectures for the main principles. The practical concepts aims for an easy conveyance of learned skills into your own NGS data analysis. The needs for analyzing plant sequence data will be a central topic for discussions.
Learning goals:
The participants will learn the basic use of UNIX, R and Perl required for downstream analysis. With these skills at hand the participants will immerse into the principles of read mapping, genome assembly and transcriptome analysis for application in plant research. The subsequent goal of statistical visualization and validation will finally emphasize to come up with a biological interpretation of the scientific data analyzed.
Prerequisites:
The crop plant specific training is aimed at advanced PhD students, postdoctoral fellows or other scientists. Basic knowledge to data formats and standards in the Omics field is beneficial. In preparation to the course introduction material will be send to the participants to gain first insights to the command line (Unix and more). Participant candidates have to write a motivation letter (max. 2000 characters) to state how they (plan to) use NGS in their work.
Keywords:
Plants, Crops, Transcriptomics, Genomics, Unix, R statistics, Read alignment, Genome assembly
Tools:
Bowtie2, TopHat, Kallisto, R, Perl, ABySS, GeMoMa, Augustus
Training material:
Contact:
Dr. Andrea Bräutigam (
Phone: +49 39482 5753