1. Copyright OpenHelix. No use or reproduction without express written consent1

2. 2 Important note to slide users: To maintain the color schemes/cues and the animations, if you import these slides into other slide sets please click the checkbox in the PowerPoint Insert window that maintains slide format. Otherwise important information may be lost. Mac usersPC users 

3. The UCSC Table Browser & Custom Tracks Advanced searching and discovery using the UCSC Table Browser and Custom Tracks Materials prepared by: Warren C Lathe, Ph.D. Updated: Q3 2008 Version 14b_0908

4. Copyright OpenHelix. No use or reproduction without express written consent4 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

5. Copyright OpenHelix. No use or reproduction without express written consent5 The Table Browser http://genome.ucsc.edu/

6. Copyright OpenHelix. No use or reproduction without express written consent6 Genome Browser Database Primary table: positions, names, etc. Underlying Database (MySQL) Auxiliary table: related data visualize search & download

7. Copyright OpenHelix. No use or reproduction without express written consent7 UCSC Genome Browser credits http://genome.ucsc.edu/goldenPath/credits.html Open Credits http://genome.ucsc.edu/staff.html Developers

8. Copyright OpenHelix. No use or reproduction without express written consent8 UCSC Genome Browser credits License

9. Copyright OpenHelix. No use or reproduction without express written consent9 UCSC Genome Browser Reference Publication Karolchik, et al. The UCSC Table Browser data retrieval tool. Nucl. Acids Res. 32(Suppl 1), D493-D496 (2004) The UCSC Table Browser data retrieval tool

10. Copyright OpenHelix. No use or reproduction without express written consent10 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Set up and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

11. Copyright OpenHelix. No use or reproduction without express written consent11 The Table Browser Open browser http://genome.ucsc.edu/

12. Copyright OpenHelix. No use or reproduction without express written consent12 Table Browser: Choose Genome In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Choose Genome In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence.

13. Copyright OpenHelix. No use or reproduction without express written consent13 Table Browser: Choose Table to Search In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Choose Data Table Custom Tracks

14. Copyright OpenHelix. No use or reproduction without express written consent14 Table Browser: Describe Table Describe table

15. Copyright OpenHelix. No use or reproduction without express written consent15 Table Browser: Choose Region to Search In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Choose Region to Search Define region

16. Copyright OpenHelix. No use or reproduction without express written consent16 Table Browser: Upload Locations to Search PasteUpload

17. Copyright OpenHelix. No use or reproduction without express written consent17 Table Browser: Filter to Refine Search Create Filter In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Submit Filter

18. Copyright OpenHelix. No use or reproduction without express written consent18 Table Browser: Output Data Output data In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence.

19. Copyright OpenHelix. No use or reproduction without express written consent19 Table Browser: Output Formats Output formats Text Fields

20. Copyright OpenHelix. No use or reproduction without express written consent20 Table Browser: Fasta Sequence Output Sequence

21. Copyright OpenHelix. No use or reproduction without express written consent21 Table Browser: Database Format Outputs Database

22. Copyright OpenHelix. No use or reproduction without express written consent22 Table Browser: Custom Track Output Custom Track

23. Copyright OpenHelix. No use or reproduction without express written consent23 Table Browser: Hyperlinks Output Hyperlinks

24. Copyright OpenHelix. No use or reproduction without express written consent24 Table Browser: Obtaining Output Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Data Summary

25. Copyright OpenHelix. No use or reproduction without express written consent25 Table Browser: Output configuration Sequence Format Get Sequence

26. Copyright OpenHelix. No use or reproduction without express written consent26 Table Browser Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

27. Copyright OpenHelix. No use or reproduction without express written consent27 Table Browser: Intersecting Data Find simple repeats (copy number > 10) within known genes and download the sequence. Intersect 2nd Table Any Overlap Submit

28. Copyright OpenHelix. No use or reproduction without express written consent28 Table Browser: Intersecting Data Narrows Search Summary Filtered simple repeats Filtered simple repeats, intersected (overlapping) w/ known genes

29. Copyright OpenHelix. No use or reproduction without express written consent29 Table Browser: Downloading Sequence Data Sequence Format Get Sequence

30. Copyright OpenHelix. No use or reproduction without express written consent30 Table Browser: Correlating Data Tables Correlate 2 Datasets Get Results

31. Copyright OpenHelix. No use or reproduction without express written consent31 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

32. Copyright OpenHelix. No use or reproduction without express written consent32 Custom Tracks: Table Browser Searches Create Track Get Output

33. Copyright OpenHelix. No use or reproduction without express written consent33 Custom Tracks: Name and Configure Track Download track file to desktop Name Track: SRepeatKGenes Describe Track: Intersection … In Genome Browser Choose default view in browser

34. Copyright OpenHelix. No use or reproduction without express written consent34 Custom Tracks: Open Track in Genome Browser Open Details Compare “…caused by an expanded, unstable trinucleotide repeat…”

35. Copyright OpenHelix. No use or reproduction without express written consent35 Custom Tracks: Track in Table Browser Custom tracks also are available for filtering and intersections on the Table Browser Custom Tracks

36. Copyright OpenHelix. No use or reproduction without express written consent36 Custom Tracks: Manage Custom Tracks Edit Track Genome Browser

37. Copyright OpenHelix. No use or reproduction without express written consent37 Custom Tracks: User-generated Data in Track Custom Tracks Link Custom Track How-to

38. Copyright OpenHelix. No use or reproduction without express written consent38 Custom Tracks: Four Steps to Create Track Four steps to create a custom track Define track characteristics Define browser characteristics Format your data Upload and view your track

39. Copyright OpenHelix. No use or reproduction without express written consent39 Custom Tracks: Track Characteristics Define Track Characteristics (step 1) track name=pairedReads description="Clone Paired Reads" visibility=3 color=0,128,0 useScore=1 Score on (1) or off (0) Default Color Default track visibility 0=hide 1=dense 2=full 3=pack 4=squish

40. Copyright OpenHelix. No use or reproduction without express written consent40 Custom Tracks: Browser Characteristics Define Genome Browser Characteristics (step 2) browser pix 620 browser hide all browser full gap browser position chr22:1000-10000 Default PositionDefault Image Width Default Track View

41. Copyright OpenHelix. No use or reproduction without express written consent41 Custom Tracks: Format your Data Format Your Data (step 3) GFF GTF PSL BED WIG Browser Extensible Data chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601

42. Copyright OpenHelix. No use or reproduction without express written consent42 Custom Tracks: Format your Data Browser Extensible Data chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512 chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601 ChromosomeStartEndNameScoreStrand Thick start Thick end ColorBlocks Block Sizes Block starts

43. Copyright OpenHelix. No use or reproduction without express written consent43 Custom Tracks: Upload Track File Upload and View your Track (step 4) Upload File

44. Copyright OpenHelix. No use or reproduction without express written consent44 Custom Tracks: Upload File from Computer Documentation template Click to browse your computer to find file

45. Copyright OpenHelix. No use or reproduction without express written consent45 Custom Tracks: Submit Track Copy and paste small or simple tracks Submit File

46. Copyright OpenHelix. No use or reproduction without express written consent46 Custom Tracks: Track Appears in Genome Browser

47. Copyright OpenHelix. No use or reproduction without express written consent47 Custom Tracks: Track Characteristics Default view of custom track is “pack” Default view of other tracks set

48. Copyright OpenHelix. No use or reproduction without express written consent48 Custom Tracks: Track Appears in Table Browser Custom Track also appears in Table Browser

49. Copyright OpenHelix. No use or reproduction without express written consent49 Custom Tracks: Genome Graphs Genome Graphs

50. Copyright OpenHelix. No use or reproduction without express written consent50 Custom Tracks: Genome Graphs Browser

51. Copyright OpenHelix. No use or reproduction without express written consent51 Custom Tracks from Outside Sources Custom Tracks Contributed Track

52. Copyright OpenHelix. No use or reproduction without express written consent52 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

53. Copyright OpenHelix. No use or reproduction without express written consent53 The Table Browser http://genome.ucsc.edu/ Open browser

54. Copyright OpenHelix. No use or reproduction without express written consent54 Table Browser: Advanced Searching Output Location Data Genomes Filter and Intersect

55. Copyright OpenHelix. No use or reproduction without express written consent55 Custom Tracks: Table Browser Searches Create Track

56. Copyright OpenHelix. No use or reproduction without express written consent56 Custom Tracks: User-generated Data in Track Custom Tracks Link Custom Track How-to

57. Copyright OpenHelix. No use or reproduction without express written consent57 Additional UCSC Genome Tools Gene Sorter Proteome Browser VisiGene In-Silico PCR

58. Copyright OpenHelix. No use or reproduction without express written consent58 Contact Information and Mailing Lists Contact Info & Mailing Lists

59. Copyright OpenHelix. No use or reproduction without express written consent59 Additional Materials available: www.openhelix.com UCSC sponsored material at www.openhelix.com/ucsc Frequently updated training presentation and exercises Self-run tutorial Quick Reference Cards Tutorials and web seminars on a number of other tools Additional sponsored bioinformatics tools coming soon Check the OpenHelix Blog for genomics resource news and information: http://www.openhelix.com/blog

60. Copyright OpenHelix. No use or reproduction without express written consent60 Table Browser and Custom Tracks Agenda Gene Sorter Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Summary Exercises UCSC Table Browser: http://genome.ucsc.edu/

61. Copyright OpenHelix. No use or reproduction without express written consent61