Agenda

1. Integrative Genomics ViewerCold Spring HarborOctober 18, 2010Jim RobinsonBroad Institute of MIT and Harvard

2. Agenda • Introduction • User Interface Basics • Data Integration • Sessions and Sharing Data • File Formats • Exercise • Importing a Genome • Exercise • Viewing Next-Generation Sequence (NGS) Data • Exercise • IGVTools • Exercise • Slides and handouts: • ftp.broadinstitute.org/pub/igv/CSH_2010

3. Introduction

4. Microarrays Epigenomics RNA-Seq NGS alignments Comparative genomics What is IGV • A desktop application for integrated visualization of multiple data types and annotations in the context of the genome

5. IGV Features • Supports integration of diverse data types, including microarray, next-generation sequencing, and sample annotations. • Allows loading from local files, the web, or DAS servers. • Scales to very large datasets on standard desktop computers. • Enables easy integration of investigator-generated datasets with public annotations and datasets hosted at the Broad and elsewhere. • .

6. IGV Web site http://www.broadinstitute.org/igv Register at http://www.broadinstitute.org/igv Click “Downloads” Click a Launch button (Mac or PC), or Download an unzip binary distribution (Linux)

7. IGV Web site http://www.broadinstitute.org/igv

8. IGV Web site Downloads page Java Web Start Binary distribution

9. User Interface Basics

10. IGV layout Cytoband Track Names Genomic Coordinates Data Panel Genome Features Annotation Heatmap

11. IGV layout NGS data Coverage Track Alignment Track

12. Tracks • Two generic types: • data (continuous valued data) • annotation (features) • Specialized types include • alignments • mutations • Type is defined by file format • Data - wig, bedGraph, igv, cn, gct, seg, tdf • Features - bed, gff, gtf, psl • Alignments – sam, bam, aligned • IGV uses type to determine • initial placement in a panel • display options

13. Annotation track UCSC style gene representation 5’ UTR Intron Exons 3’ UTR Zoomed in views

14. Annotation display mode 1. Features are drawn in a single row, by default 2. Expand the track using the popup menu

15. UI basics • Selecting a reference genome • Loading data • Navigating through the data • Setting track attributes

16. Selecting a reference genome • (1) IGV provides a set of hosted genomes • Choose one of the hosted genomes from the pull-down menu • For more information about available genomes, see www.broadinstitute.org/igv/Genomes • (2) You can import other genomes and custom assemblies

17. Loading data • Data types • Any data tied to genomic coordinates • Genome annotations • Sample attributes • File formats • Many different file formats supported • See www.broadinstitute.org/igv/FileFormats • File names • File name extensions are used by IGV to determine file type • Data sources • Local files • URLs • IGV data server (Broad IGV server or other) • DAS

18. Loading data • #1 : Load local file • #2 : Load from URL • #3 : Load from server • (Broad IGV data server, other data server) • #4: Load from DAS

19. “Load from server” menu • What you see depends on : • (1) which server you selected – default is Broad server • (2) which reference genome you’ve selected • Click on the for more information about the data source

20. “Load from server” menu • What you see depends on : • (1) which server you selected – default is Broad server • (2) which reference genome you’ve selected • Click on the for more information about the data source • Click on the to expand the sub-menus

21. “Load from server” menu • Click on the to select datasets • Note that all nested datasets are also selected – make sure you know what you’ve selected

22. “Load from server” menu • NOTE… • … you cannot unload using the checkboxes

23. Navigating Whole genome view

24. Navigating Zooming in to the chromosome level Select chromosome from menu Click on chromosome number

25. Navigating Chromosome view

26. Navigating Zooming further in Use the railroad track Specify range in the search box Click and drag in the genome ruler Double-click in the data panel Shift-click to go faster Alt-click to zoom back out

27. Navigating Move to location at same zoom level Click on cytoband Click on ruler Click and drag in the data panel – up/down left/right Use scroll bar Use keyboard (1) arrow keys (2) Page Up, Page Down, Home, End

28. Setting track attributes Right-click popup menu

29. Setting track attributes Multiple tracks Select multiple tracks by clicking on track names : Shift-click / Ctrl-click Select multiple tracks by clicking on color in annotation heatmap

30. Setting track attributes Global attributes

31. Data Integration

32. Data integration • Load different types of data • Use sample annotations to manipulate tracks • Sort • Group • Filter

33. Sample annotations • Default annotations for all sample tracks: • data file, data type, track name • Custom annotations: • use sample information file • Show / hide annotation panel • (View > Show Attribute Display) • Show / hide selected annotations • (View > Select Attributes to Show)

34. Sort tracks by sample annotation Click on the annotation name Use the menu Tracks > Sort Tracks

35. Sort tracks by data value in a region Region selection tool Popup menu

36. Group tracks

37. Group tracks

38. Group tracks

39. Filter tracks

40. Filter tracks

41. Filter tracks

42. Gene/locus list views • Version 2.0 (late 2010) will include a Gene/Locus list view see http://www.broadinstitute.org/software/igv/wiki • Example: RTK/RAS signaling genes

43. Sessions and Sharing Data

44. Sessions • Save current state of IGV to a named session file. • Use to • restore the same state • share session with colleagues

45. Sharing data • Make your data file available via HTTP • Use HTML hyperlinks to launch IGV and share datasets over the Web • Configure your own data server

46. Creating Web links to launch IGV Use HTML hyperlinks to launch IGV and share datasets over the web. Two types of links are supported (1) Launch IGV on a specified session file. Example: http://www.broadinstitute.org/igv/dynsession/igv.jnlp?sessionURL=http://www.broadinstitute.org/tumorscape/textReader/IGV/all_tumors_session.xml&locus=chr7:55054218-55206232 (2) Load sessions or data files into a running IGV Example: http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&locus=egfr&genome=hg18

47. Configuring a data server • Create a custom “Load from Server” menu. • A separate XML file describes each item under Available Datasets. • (2) Create a registry file that lists the XML files. • (3) Use IGV Preferences to use your registry instead of the IGV default.

48. Configuring a data server • Create a custom “Load from Server” menu. • A separate XML file describes each item under Available Datasets. • Example: • <?xml version="1.0" encoding="UTF-8"?><Global name="Example Project"  • hyperlink="http://www.broadinstitute.org/igv/" • version="1">    <Category name="Category">        <Category name="Subcategory One">        <Resource name="pi.12mer.tdf"                  path="http://www.broadinstitute.org/igvdata/pi.12mer.tdf" />        </Category>        <Category name="Subcategory One">        <Resource name="omega.12mer.tdf"                  path="http://www.broadinstitute.org/igvdata/omega.12mer.tdf" />        </Category>    </Category> </Global>

49. Configuring a data server • (2) Create a registry file that lists the XML files. • Example: • http://www.broadinstitute.org/igvdata/annotations/hg18/hg18_annotations.xmlhttp://www.broadinstitute.org/igvdata/tcga_external.xmlhttp://www.broadinstitute.org/igvdata/mmgp.xmlhttp://www.broadinstitute.org/igvdata/epigenetics_public.xmlhttp://www.broadinstitute.org/igvdata/1KG/1KG.xmlhttp://www.mycompany.org/igvdata/example_project.xml

50. Configuring a data server • Use IGV Preferences to use your registry instead of the IGV default. • View > Preferences : Advanced tab