ideas4biologyNGS in Medical Research

This is a crush course on a complete, standard RNA-Seq and genome re-sequencing data analysis. It includes quality control and filtering, read mapping, estimation of gene expression values, differential expression analysis, variant calling, filtering and annotation – providing ready to use solutions for the most popular and essential omics approaches in medical research.

Target

This is an introductory course for anyone whose aim is to learn how to deal with large-scale RNA-Seq and genome re-sequencing data data and to obtain scientifically relevant insights. It is tailored for those who work in the fields of medicine and molecular biology, or any other biological sciences, yet anyone can participate. Prior knowledge of NGS data analysis is not essential, however it is advised that the participants know basics of molecular biology, such as what is splicing, splicing isoform, transcriptome, gene expression etc. Also, no programming skills are required.

Expected effects

Upon completion of the workshop, the participants should know about NGS data sources, their formats, and be able to perform data quality control, read mapping to a reference, estimate gene/transcript expression values, and perform differential expression analysis, including interpretation of obtained results. The participants will also learn about variant calling and annotation and will be able to apply analytical pipelines in their own projects. Also, much emphasis will be put on data visualization, plotting, interpretation, and troubleshooting.

Yes, You can participate!

No programming skills are required. Also, prior knowledge of NGS data analysis is not essential, however it’s advised that the participants know basics of molecular biology, such as what is splicing, splicing isoform, transcriptome, gene expression etc.



ideas4biologyDetails

PART 1: Linux for bioinformatics (1 day)

This module introduces a Linux operating system, a powerful– yet often discouraging – environment for bioinformatics applications, such as NGS data processing. We will learn about commands that help working on huge datasets, including search and browsing of NGS-related data. We will learn basics of scripting and exercise various commands that enable automatization and control of data flow during a bioinformatics application. After a single day you should feel quite comfortable using this operating system and be well prepared for the following bioinformatics applications.

PART 2: Introduction to NGS data analysis (1 day)

This is an introductory course to NGS data processing: starting with raw sequencing results in a FASTQ format, through different methods for data quality check, filtering, adapter trimming and read mapping to finally assemble a transcriptome. In a single day, you will learn a complete, functional pipeline for NGS application. Additionally, NGS-related formats, databases and knowledge bases will be discussed.

PART 3: RNA-seq data analysis in medical research (1 day)

Alternative approaches for RNA-Seq data processing will be discussed and executed, including estimation of gene and transcript expression levels, differential expression analysis. Essential diagnostic plots and quality checks will be done.

PART 4: Variant calling and annotation (1 day)

Germline and somatic mutations will be identified from Whole Genome Sequencing data, including single nucleotide variants, insertions, deletions and copy number variants. The results will be subject to functional annotation, filtering and compared against public databases, allowing comprehensive interpretation of the identified variants.



ideas4biologyAbout us

We have been on the market since July 2013 and since then we have organized dozens of bioinformatics workshops with almost one thousand of participants altogether. We have completed a number of NGS projects for our customers, which included model and non-model organisms, from bacteria to human. We are a part of consortium aiming at development of personalized medicine services for diagnosis and therapy of lung cancer. We are also conducting academic research in the area of genomics and transcriptomics, which provides us with expertise on standard and up-to-date bioinformatics solutions.




ideas4biologySpeakers

  • Izabela Makałowska (Professor, CEO at ideas4Biology Ltd., Head of the Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University in Poznan)
  • Michał Szcześniak (PhD, Deputy CEO at ideas4biology Ltd., University Adjunct at the Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University in Poznan)
  • Joanna Ciomborowska-Basheer (PhD, Deputy CEO at ideas4biology Ltd., University Adjunct at the Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University in Poznan)
  • Maciej Osowiecki (BSc, Junior Data Scientist at ideas4biology Ltd.)
  • Jan Kosiński (BSc, Junior Data Scientist at ideas4biology Ltd.)





ideas4biologyPoznań

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ideas4biologyCONTACT US

EMAIL
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