1. IGV Demo Slides:/g/funcgen/trainings/visualization/Demos/IGV_demo.ppt Galaxy Dev:http://gbcs-dev.embl.de/galaxy-dev/ 0

2. What is IGV? Elaborated as ‘Integrative Genomics Viewer’. Integrated visualization tool for multiple data types and genome annotations. Data from NGS analysis visualized. 1

3. Why use IGV? Handles large datasets Interactive and speedy visualization. Run locally on desktop View multiple datasets in separate panels on the same pane. Several track management options (filtering, grouping, sorting) and in-built tools (index, sort, motif finder…) Direct visualization from Galaxy : bed, wig, gff, gff3, Bam, bigWig, bigBed, vcf formats. 2

4. Visualizing Galaxy Datasets In IGV 3

5. Importing Shared Data Libraries into Galaxy ‘History’ Import both datasets from Shared Data->Data Libraries->Training into your preferred ‘history’. 4 1 1 2 2 3 3

6. Visualizing Galaxy datasets in IGV To visualize in the locally running IGV Downloads IGV as a JNLP file on your system. Locate the file and double-click on it to visualize. 5 To visualize any dataset from your Galaxy History into IGV, you have two options: web current and local. Look for UCSC_all_mrna_chr4.bed dataset in the RNA-Seq Visualization dataset and select ‘web current’.

7. Visualizing Galaxy datasets in IGV(2) Select the ‘web current’ option for IGV, open the downloaded jnlp file with ‘Java Web Start’, and you will be asked for authentication. Please enter your embl username and password. 6

8. Visualizing Galaxy datasets in IGV(3) 7 This is what you should be able to visualize at first. Select chr4 from the drop down menu in the upper left corner, as the dm3 datasets used for this training only contain chr4 data.

9. Launching JNLP files You can change your computer settings to always launch the jnlp files with Java Web Start. For Operating System: Safari before 6.0.3 1.Make sure you have the JRE installed 2.Locate jnlp in Finder 3.Click on "Get Info" 4."Open with " and select ‘Java Web Start’ 5.Change all For Operating System: Safari after 6.0.3 Please follow the links below. http://derflounder.wordpress.com/2013/03/16/automatically-enable-the-java- web-plug-ins-setting-in-safari-6-0-3-and-later/ http://derflounder.wordpress.com/2013/03/16/automatically-enable-the-java- web-plug-ins-setting-in-safari-6-0-3-and-later/ http://derflounder.wordpress.com/2012/04/13/automatically-activate-the-java- web-plug-ins-setting-on-login/ http://derflounder.wordpress.com/2012/04/13/automatically-activate-the-java- web-plug-ins-setting-on-login/ 8

10. Launching JNLP Files (2) For Operating System: Chrome Autostart enabled for jnlp files. For Operating System: Firefox Please follow the link below. http://pic.dhe.ibm.com/infocenter/director/pubs/index.jsp?topic=%2Fco m.ibm.director.console.helps.doc%2Ffqm0_t_associating_the_jnlp_file_ty pe_with_jws_firefox.html http://pic.dhe.ibm.com/infocenter/director/pubs/index.jsp?topic=%2Fco m.ibm.director.console.helps.doc%2Ffqm0_t_associating_the_jnlp_file_ty pe_with_jws_firefox.html 9

11. Visualizing Library datasets : chr4 D.melanogaster 10 Choose to display the Bam, Bed, Wig and bigwig files from the Data Library ‘Training’ (RNA-Seq and CHIP-Seq folders) in Galaxy on IGV ‘local’. All the files will be visualized on the same pane. Wig- MACS bigwig bed

12. Zooming in on the datasets 11 You can zoom in and out on the datasets by using the slider on the upper-right corner of the pane. Use the ‘+’ sign to zoom in and ‘-’ sign to zoom out. CHIP- Seq Bam RNA-Seq Bam

13. IGV Features 12

14. Showing all bases 13 To show all the bases in a track, right-click on the track and select ‘Show all bases’.

15. Visualizing SAM files in IGV:igvtools 14 To visualize a SAM file in IGV, you need to create a sai index using Tools-> Run igvtools. 1 1 2 2 From the drop-down menu of ‘Command’, select ‘Index’ 3 3 Select your input SAM file and hit ‘Run’. You can download the ‘mapped4.sam’ file from the ‘Training’ library in Galaxy.

16. Visualizing a SAM file 15

17. Saving sessions 16 Save your session by clicking on the IGV File Menu and selecting ‘Save Session’. The session will be saved as a xml file and you can re-open it later by selecting ‘Open Session’.

18. Session File A session file (XML) contains information about the genome, locus, data files opened in IGV when the session was saved. It also contains detailed information about the tracks which were saved. Session can be easily restored in IGV at a later point. 17

19. Exploring IGV using Cancer data from the IGV Server 18

20. Loading data from Server Open a new session from the File menu. Select the desired genome (Human hg19) from the drop down menu on the upper left corner. 1. Or choose to load the genome from File, URL or Server by clicking on ‘Genomes’ in the IGV Menu 19

21. Loading data from Server (2) 2.2. 2.2. Choose to load the file from Server. Other options include loading from File or URL. 3 3 The available datasets can be seen. Select the desired one, for instance, ‘The Cancer Genome Atlas’. 20

22. Loading data from Server (3) 4 4 Check to see the contents of the dataset and select the desired sub-sets. The selected sub-sets for this demo are shown below. 21

23. Whole genome view The whole genome can be visualized by selecting the ‘All’ option from the Chromosome drop-down menu in the Tool Bar. Use keyboard (1) arrow keys (2) Page Up, Page Down, Home, End for navigating. 22

24. Viewing a specific chromosome Zoom Slider Range of chromosome position Cytoband box showing current position Ruler Track names Genome Features Annotation Heatmap Data Panel 23 Select ‘chr1’ to view data from Chromosome 1. You can also enter a range of chromosome position.

25. Changing Track settings 24 Right click on a track to change the settings.

26. Changing Track Settings (2) 25

27. Changing Track Settings(3) 26 Expanding the Collapsed Tracks Expanded Tracks Squished tracks

28. Grouping Tracks by Attributes 27 Select ‘Group Tracks’ from the ‘Tracks’ menu to group tracks by attributes – Name,Data type,Data file or sample, in this case. Choose to group tracks by Data type.

29. Tracks grouped by Data Type 28 Shown below are tracks grouped by the attribute ‘Data Type’.

30. Sorting Tracks by Attributes 29 Choose to sort tracks by ‘Data File’ in ascending order. Select ‘Sort Tracks’ from the ‘Tracks’ menu to sort tracks by attributes- Name, Data type, Data file or Sample, in this case.

31. Tracks Sorted by Data File 30

32. Filtering tracks by Attributes 31 Select ‘Filter Tracks’ from the ‘Tracks’ menu and choose to filter them by name, Data Type, Data File or sample. For example, choose to filter by attribute-Data type, containing the term ‘Copy’.

33. Tracks filtered by Attribute-Data Type 32 Tracks with Data type –Copy number shown below.

34. Specific Search 33 A specific region or feature can be typed in the search box for direct navigation. For example, type ‘egfr’ in the search box.

35. Specific Search(2) 34 You will be navigated to the specific search.

36. Save and Exit 35

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