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Genomic data visualization

Aim

​The aim of this workshop is to provide participants with the necessary skills to understand how to visualize and interpret complex genomic datasets. The workshop will introduce to UCSC Genome Browser, Integrative Genomics Viewer (IGV) and Genomic Visualization in R (GenVisR).

Topics include

  • High-throughput genomic datasets and file formats (FASTA, GTF, BED, VCF, MAF, BAM,…)
  • UCSC Genome Browser:
    - Graphical view of genes, gene structure, and public annotation tracks (expression, variation, regulation,…)
    - Custom Tracks - uploading and displaying the own data in the Browser
    - Introduction to Track Hubs
     
  • Integrative Genomics Viewer (IGV): •Loading a genome and data (RNA-seq, Chip-seq,…)
    - Visualization read alignment
    - Inspecting variants (SNPs, SNPs, SVs)
    - Sashimi Plot
    - Automating tasks
     
  • Genomic Visualizations in R (GenVisR): cohort level genome analyses:
    - Visualization of small variants: waterfall (mutation overview graphic), lolliplot (mutation hotspot graphic)
    - Copy number alterations (cnSpec, cnView)

The detailed schedule will be distributed to accepted participants prior to the start of the workshop.

Number of participants

5-10

Entry requirements

  • Participants are expected to use their own computers.
  • R programming (RStudio)
  • IGV on the laptop
  • UCSC Genome Browser account

This workshop is organised by the Research School in Stem Cell Biology in collaboration with the StemTherapy Bioinformatics Core Facility. Please be aware that the number of participants is limited. Participation in the workshop is free of charge for members of the Research School in Stem Cell Biology.

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WHEN AND WHERE?

March 19, 2019 at 13.00 - 17.00

Venue: BMC I1308

WORKSHOP LEADER

Phuong Cao Thi Ngoc
Computational biologist, RNA and Stem Cell Biology Lab

Email: phuong [dot] cao_thi_ngoc [at] med [dot] lu [dot] se

Teaching assistant

Jonas Ungerbäck
Senior postdoc, Molecular Lymphopoiesis Lab

Email: Jonas [dot] Ungerback [at] med [dot] lu [dot] se

APPLICATION

Applications will open on November 14, 2018 and will run until December 5, 2018.

Applicants will be informed of the outcome of their application via email within one week after the application deadline.