Teaching at the NIHES NGS course
On Monday March 5 2018, I will be teaching at the NIHES course “An Introduction to the Analysis of Next-Generation Sequencing data” at the Erasmus Medical Centre in Rotterdam. In this one-week course students will learn the basics of how NGS data is generated and how to analyse this type of data.
PolyOmica’s contribution to the course will be an introduction to working on the Linux command line and a lecture on the basic file formats used when working with NGS data. In the first lecture I will cover the basics of working on the Linux command line, for example, how to connect to a remote server, the typical Linux file system layout, how to create and move around directories, how to copy and move files, how to transfer data to and from a remote server, etc. In the file formats lecture, I will discuss a typical NGS pipeline and show where e.g. FASTQ files, BAM files and VCF files appear, what (roughly) look like and what they are used for. Both lectures will be accompanied by exercises to give the students hands-on experience.
During the remaining days of the week, other teachers will cover topics on SNP calling, annotation and imputation of structural variants, (meta-) analysis of rare genetic variants using seqMeta, and analysis of family-based sequence data.
So if you are in the neighbourhood of the Erasmus MC next week, let us know! It would be great to have a chat.
Image source: User Huee on Creative Commons.org, CC-BY 2.0 licence.