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
- Introduction to Next-Generation-Sequencing
- Quality control on raw data
- Assembling a small genome sequence
- Assembly QC
- Annotating genes
- Using long reads for assembly
- Hybrid Assembly QC
- Experimental design and strategies
- Data cleaning + mapping
- Quantification
- Visualization
Thursday - 22th of August, Building 3, Level 5, Room 5220: 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
TBA