Introduction to Integrative Genomics Viewer for NGS Analysis

Introduction to Integrative Genomics Viewer for NGS Analysis 劉傳崑 chuankun@ibms. sinica. edu. tw 中央研究院 國家基因體醫學研究中心 2013/09/06

Agenda • • • 認識 Integrative Genomics Viewer 如何啟動 IGV? 如何使用 IGV瀏覽 NGS測序分析結果? Hi. Pipe與 IGV的相遇 總結

無線網路與 FTP主機 會議室無線網路 1. SSID: hipipe_A 2. SSID: hipipe_B 3. SSID: B 1 B Hi. Pipe 教育訓練主機 http: //10. 69. X Demo Data Task ID: f 499264 b-bd 61 -4 d 31 -97 c 2 -b 088 c 5 f 106 a 4 教育訓練課程 FTP主機 瀏覽器網址列輸入 ftp: //10. 69. X/download/ 1. 簡報檔 – IGV_20130906. pdf 2. 1000 Genomes (Demo Data) – Integrated_call_samples. 20101123. ped 3. igv – IGV_2. 3. 17. zip 4. java – – – jre-7 u 25 -windows-x 64. exe (64位元 Windows) jre-7 u 25 -windows-i 586. exe (32位元 Windows) jre-7 u 25 -macosx-x 64. dmg (Mac. OS X)

認識 Integrative Genomics Viewer

IGV的相關文件 Thorvaldsdóttir, H. et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics (2012). Robinson, J. T. et al. Integrative Genomics Viewer. Nature Biotechnology 29, 24 -26 (2011).

如何安裝 Java http: //www. java. com

The IGV application window Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

選定參考 Genome • 預設為 Human hg 18 • 點選 More…增加其他 Genome • Load Genome from file…

File Formats

瀏覽 VCF與 BAM

瀏覽 VCF與 BAM

VCF Track I The allele fraction A CGT

VCF Track II Heterozygous Homozygous Reference A CGT

Read alignment views at 20 kb and base pair resolution Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

清除 IGV已載入的資料 File -> New Session… 在 Track上按滑鼠右鍵 -> Remove Track

Load Data from URL

Load Data from Server

The attribute panel displays a color-coded matrix of phenotypic and clinical data Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

The attribute file • a tab-delimited text file

Group Tracks

Visualization of RNA-seq data from heart and liver tissue samples All junctions with more than 50 reads have the same thickness. Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

Gene-list view of copy number, mutation and clinical data from 202 glioblastoma samples from the TCGA project Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

Gene-list View

Interpreting Color by Insert Size • Red for an inferred insert size that is larger than expected (deletion) • Blue for an inferred insert size that is smaller than expected (insertion)

Split-screen view of read alignments from a glioblastoma multiforme tumor sample and matched normal, displaying regions of chromosomes 1 and 6 Thorvaldsdóttir H et al. Brief Bioinform 2013; 14: 178 -192 © The Author(s) 2012. Published by Oxford University Press.

Interpretation of read pair orientations Inversions Tandem Duplication

Hi. Pipe與 IGV的相遇

Hi. Pipe http: //hipipe. ncgm. sinica. edu. tw

Step 1 : Keep the task ID

Step 2 : Set up Parameters

Step 3 : Upload Sequence Data

Step 4 : Check Sequence Data Upoaled unpaired file

Monitor

Result - Summarize

Result - Browse

Integrative Genomics Viewer Variants Coverage Reads Genes

Result - Download

Performance (Human) Estimated Note Analysis Time Whole Genome 8 -10 Hours 30 x Coverage Exome 1 -2 Hours 100 x Coverage Transcriptome (Dec. , 2013) Micro. RNA (Dec. , 2013) 2 -5 days 12 * 2 Gbp (Paired Sample) 3 Gbp 3 -5 Hours

Thanks for your attention!