A Practical Introduction to Data Analysis for Genomics and Transcriptomics - KAUST 2019
Table of Content
Genomics and transcriptomics are rapidly becoming standard methods to examine living systems. This workshop provides an introduction to the methods and tools used to analyse next-generation-sequencing data, provides understanding of its limitations and a basic understanding on how the analysis algorithms work. This workshop will take the participants through an example project demonstrating how to evaluate the quality of data as provided by a sequencing facility, how to perform a de-novo genome assembly, and how to align the data against a known and annotated reference genome. Furthermore, participants will learn how to compare transcription data between different samples.
The workshop is scheduled for 18th - 22nd of August, from 9:30 to 17:00, and will consist of seminars intertwined with hands-on sessions and discussions. The course is open for all students, postdocs and research scientists of BESE division.
Major topics to be covered: Genome assembly, Transcriptomics, Visualization and Tips/tricks.
- Introduction to programming basics
- Utility commands in data management
- Common file formats in NGS data
- Introduction to High-Performance Computing environment
Monday - 19th of August, Building 5, Level 5, Room 5520: Where do the data come from?
- Introduction to Next-Generation-Sequencing
- Quality control on raw data
- Assembling a small genome sequence
Tuesday - 20th of August, Building 3, Level 5, Room 5520: How to make a genome
- Assembly QC
- Annotating genes
- Using long reads for assembly
- Hybrid Assembly QC
Wednesday - 21th of August, Building 3, Level 5, Room 5520: How to quantify transcription
- Experimental design and strategies
- Data cleaning + mapping
Thursday - 22th of August, Building 3, Level 5, Room 5520: How to compare transcription between samples
- Differential expression
- Functional annotation
- Alternative splicing
- Summary + QA + Recap
- Arun Nagarajan, PostDoc at KAUST, is interested in understanding the molecular mechanism of acclimatization to stress by a biological organism using new-age technology.
- Robert Lehmann, Research Scientist at KAUST, integrates genetic and transcriptomic data to gain insights into genetic responses to stress in established model organisms as well as new marine model organisms.
- Octavio Salazar Moya, PostDoc at KAUST, is interested in increasing food production, particularly by increasing salt tolerance of plants.
- Manjula Thimma, Research Scientist at KAUST, is interested in understanding the role of retrotransposons in cell identity, reprogramming and differentiation.
- Alaguraj Veluchamy, Research Scientist at KAUST, is interested in TBA
- Aug 18–19 Building 5, Level 5, Room 5520
- Aug 20-22 Building 3, Level 5, Room 5520