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Bioinformatic Analysis of Next Generation Sequencing Data

April 14-17,2020


National Institutes of Health

9000 Rockville Pike

Building 60, Room 162

Bethesda, MD 20892, USA


Participants will start with a general introduction to the NGS data analysis concepts, methods and tools, followed by a gentle biologist friendly Linux hands-on training.An NGS expert will then walk through

  • a. RNA-Seq analysis starting with QC, preprocessing, alignment, transcript quantification, differential expression and downstream analysis/visualization
  • b. DNA-Seq variant calling analysis with QC, alignment, variant calling, variant filtering and annotation
  • c. ChIP-Seq analysis with peak calling, peak annotation, motif analysis
  • d. Integration of NGS data using Network analysis methods and tools.


Next generation sequencing technologies are producing enormous amount of sequencing data. Analyzing this massive amount of data requires the ability to use the sophisticated tools and techniques in the Unix platform. This course will introduce the participants to the skills needed to get started with their NGS data analysis journey.


  • Participants will use a Graphic User Interface based Linux Desktop environment, specially configured for NGS data analysis in the cloud
  • Training provided by experienced active NIH researchers
  • Cookbook style bound manual for all exercises
  • Continuing Education Credits

Hands-on Skills/Tools taught

  • Basic Linux Skills
  • QC: FastQC
  • Pre-Processing: Trimmomatic
  • Alignment: BWA, HISAT2
  • Transcript Quantification: StringTie
  • Differential Expression Analysis: BallGown
  • Visualization: Samtools, RStudio
  • Variant Calling: GATK
  • Variant Annotation: VEP
  • Peak Calling: MACS2
  • Motif Finding: MEME
  • Downstream Analysis: UCSC Table Browser, DAVID
  • Network Analysis: Cytoscape, STRING
  • Utilities: Picard, Samtools, Galaxy, BCFTools

For more information and registration, please visit the following page;
Information and Registration



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