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Exome-Seq Data Analysis Workshop
The cost of next generation sequencing (NGS) has fallen rapidly, allowing NGS to be routinely applied within research or clinical genetics laboratories. Whole Exome Sequencing (WES) utilizes NGS to sequence all the protein coding regions of the genome in a single assay. Performing WES can be more cost effective than performing multiple, smaller sequencing experiments, each with a panel of genes. However, adoption of NGS introduces new bioinformatics challenges to laboratories, requiring a new skill set to enable data to be processed, analyzed and interpreted correctly. This workshop will introduce the UNIX command line, the platform on which many bioinformatics tools are designed to run on, before outlining and exploring the steps of a bioinformatics pipeline. In lectures and practical’s the tools applied to map reads to a reference, call and annotate variants will be explored, examining the data formats produced at each step and how to ensure data meets quality control. Clinical scenarios will then be used to analyze and interpret variants, including the design and application of gene panels, use of public datasets and in silico prediction tools. Whilst the work shop will be clinically focused, the tools applied and challenges faced are equally applicable to the research environment.
After this workshop participants should:
- More familiar with the tools and means to construct workflows/pipelines for WES data analysis
- To understand the file formats produced at each stage of the bioinformatics pipeline (BAM, fastq, vcf).
- To gain practical skills in applying standard bioinformatics tools, such as alignment to a reference sequence, variant calling and annotation.
- To identify genes associated with a phenotype to design a gene panel which can be applied to whole exome data.
- Gain experience in analysis and interpretation of NGS variants
- Understand the quality control of sequencing data.
- Introduction to NGS analysis methods
- Introduction to R and UNIX
- Raw Data Selection (NGS Data selection, principles, type of data, file formats)
- Quality analysis of raw data
- Pre-processing of raw data (Trim adaptors & Contaminants, Filter by quality scores, filter duplicate reads)
- Mapping reads onto a reference genome
- Targeted sequencing quality control
- Quality control of mapped reads
- Post alignment processing
- Variant calling
- Effect annotation of the found variants
- Variant prioritization in Variant Explorer
Last date for Registration: 21 January, 2018
Faculty Members: 5000/-
Industrial People: 7000/-
Call/ SMS / Whatsapp to +91-9844158444 Or Email with Name, Phone number, Email address, University/College/Institution, Address, Field of study, References to email@example.com web link www.scientificbiominds.in
- Participants are encouraged to bring their own laptops with UBUNTU system
- Wifi facility is provided
- Participants need accommadation please contact Dr.C.N.Prashanth +91-9844158444
- Study materials, Workshop related softwares will be provided