1. The UCSC Table Browser & Custom Tracks Advanced searching and discovery using the UCSC Table Browser and Custom Tracks Osvaldo Graña CNIO Bioinformatics Unit Materials prepared by: Warren C Lathe, Ph.D. Version 19b

2. Copyright OpenHelix. No use or reproduction without express written consent2 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Exercises UCSC Table Browser: http://genome.ucsc.edu/

3. Copyright OpenHelix. No use or reproduction without express written consent3 The Table Browser http://genome.ucsc.edu/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Genome Browser Database Primary table: positions, names, etc. Underlying Database (MySQL) Auxiliary table: related data visualize search & download

5. Copyright OpenHelix. No use or reproduction without express written consent5 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

6. Copyright OpenHelix. No use or reproduction without express written consent6 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/

7. Copyright OpenHelix. No use or reproduction without express written consent7 Discovery using the Table Browser McMurray, C. Mechanisms of trinucleotide repeat instability during human development. Nature Reviews Genetics 11: 786-99

8. Copyright OpenHelix. No use or reproduction without express written consent8 The Table Browser Open browser http://genome.ucsc.edu/

9. Copyright OpenHelix. No use or reproduction without express written consent9 Table Browser: Choose Genome Choose Genome In the Human genome, search for simple repeats in the entire genome with the exact sequence “CAG” and get table data.

10. Copyright OpenHelix. No use or reproduction without express written consent10 Table Browser: Choose Table to Search Choose Data Table In the Human genome, search for simple repeats in the entire genome with the exact sequence “CAG” and get table data.

11. Copyright OpenHelix. No use or reproduction without express written consent 11 Table Browser: Describe Table Describe table

12. In the Human genome, search for simple repeats in the entire genome with the exact sequence “CAG” and get table data. Copyright OpenHelix. No use or reproduction without express written consent 12 Table Browser: Choose Region to Search Choose Region to Search Define region

13. Copyright OpenHelix. No use or reproduction without express written consent13 Table Browser: Upload Locations to Search PasteUpload

14. Copyright OpenHelix. No use or reproduction without express written consent14 Table Browser: Quick Summary of Expected Hits Data Summary Nearly 1 million simple Repeats annotated in the Human genome

15. In the Human genome, search for simple repeats in the entire genome with the exact sequence “CAG” and get table data. Copyright OpenHelix. No use or reproduction without express written consent15 Table Browser: Filter to Refine Search Create Filter Submit Filter Delete wildcard “*” and type in “CAG” (uppercase)

16. Copyright OpenHelix. No use or reproduction without express written consent16 Table Browser: Output Data Output data In the Human genome, search for simple repeats in the entire genome with the exact sequence “CAG” and get table data.

17. Copyright OpenHelix. No use or reproduction without express written consent17 Table Browser: Output Formats Output formats Text Fields

18. Copyright OpenHelix. No use or reproduction without express written consent18 Table Browser: Fasta Sequence Output Sequence

19. Copyright OpenHelix. No use or reproduction without express written consent19 Table Browser: Database Format Outputs Database

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

21. Copyright OpenHelix. No use or reproduction without express written consent21 Table Browser: Hyperlinks Output Hyperlinks

22. Copyright OpenHelix. No use or reproduction without express written consent22 Table Browser: Obtaining Output Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Data Summary 80 simple repeats in the genome match our filter criteria, out of 1 million

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

24. Copyright OpenHelix. No use or reproduction without express written consent24 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Exercises UCSC Table Browser: http://genome.ucsc.edu/

25. Copyright OpenHelix. No use or reproduction without express written consent25 Table Browser: Intersecting Data Find simple repeats (sequence = CAG) within known genes and get hyperlinks. Intersect 2nd Table Any Overlap Submit

26. Copyright OpenHelix. No use or reproduction without express written consent26 Table Browser: Intersecting Data Narrows Search Summary Filtered simple repeats Filtered simple repeats, intersected (overlapping) w/ known genes

27. Copyright OpenHelix. No use or reproduction without express written consent27 Table Browser: Get hyperlinks get output

28. Copyright OpenHelix. No use or reproduction without express written consent28 Table Browser: Exploring the results HTT, chr4: 307… CAG Q ATN1, chr12: 704…CAG Q

29. Copyright OpenHelix. No use or reproduction without express written consent29 Table Browser: Exploring the results RAI1 CAG Q DMPK

30. Copyright OpenHelix. No use or reproduction without express written consent30 Table Browser: Exploring the results CAG DMPK Direction of transcription CTG

31. Copyright OpenHelix. No use or reproduction without express written consent31 The Table Browser McMurray, C. Mechanisms of trinucleotide repeat instability during human development. Nature Reviews Genetics 11: 786-99

32. Copyright OpenHelix. No use or reproduction without express written consent32 Table Browser: Correlating Data Tables Correlate 2 Datasets Get Results

33. Copyright OpenHelix. No use or reproduction without express written consent33 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Exercises UCSC Table Browser: http://genome.ucsc.edu/

34. Copyright OpenHelix. No use or reproduction without express written consent34 Custom Tracks: Table Browser Searches Create Track Get Output

35. Copyright OpenHelix. No use or reproduction without express written consent35 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

36. Copyright OpenHelix. No use or reproduction without express written consent36 Custom Tracks: Open Track in Genome Browser Open Details Compare “…caused by an expanded, unstable trinucleotide repeat…”

37. Copyright OpenHelix. No use or reproduction without express written consent37 Custom Tracks: Track in Table Browser Custom tracks also are available for filtering and intersections on the Table Browser Custom Tracks

38. Copyright OpenHelix. No use or reproduction without express written consent38 Custom Tracks: Manage Custom Tracks Edit Track Genome Browser

39. Copyright OpenHelix. No use or reproduction without express written consent39 Custom Tracks: User-generated Data in Track Custom Track How-to

40. Copyright OpenHelix. No use or reproduction without express written consent40 Custom Tracks: Four Steps to Create Track Four steps to create a custom track Format your data Define browser characteristics Define track characteristics Upload and view your track Add URL for annotation details (option) http://genome.ucsc.edu/goldenPath/help/customTrack.html

41. Copyright OpenHelix. No use or reproduction without express written consent41 Custom Tracks: Format your Data Format Your Data (step 1) GFF GTF PSL BED WIG bigBED bigWIG Etc... Browser Extensible Data chr4 56010000 56015000 cloneA 900 + chr4 56014000 56019000 cloneB 200 + chr4 56017000 56023000 cloneC 800 - chr4 56021000 56028000 cloneD 300 -

42. Copyright OpenHelix. No use or reproduction without express written consent42 Custom Tracks: Format your Data Browser Extensible Data: 3 required fields, 9 optional fields chr4 56010000 56015000 cloneA 900 + chr4 56014000 56019000 cloneB 200 + chr4 56017000 56023000 cloneC 800 - chr4 56021000 56028000 cloneD 300 - Chromosome Start En d Name Score (shading) Additional optional fields: Thick region, Item color, Number of blocks, size of blocks, start position of blocks Strand

43. Copyright OpenHelix. No use or reproduction without express written consent43 Custom Tracks: Browser Characteristics Define Genome Browser Characteristics (step 2) browser position chr4:56010000-56030000 browser pix 800 browser hide all browser pack snp130 browser full knownGene Default PositionDefault Image Width Default Track View

44. Copyright OpenHelix. No use or reproduction without express written consent44 Custom Tracks: Track Characteristics Define Track Characteristics (step 3) Score on (1) or off (0) Default Color Default track visibility 0=hide 1=dense 2=full 3=pack 4=squish track name=clones description="Clones" visibility=2 color=200,0,200 useScore=1 db=hg18 Database Can also define group placement, turn item colors on, and more.

45. Copyright OpenHelix. No use or reproduction without express written consent45 Custom Tracks: The Track File Our Track: browser position chr4:56010000-56030000 browser pix 800 browser hide all browser pack snp130 browser full knownGene track name=clones description="Clones" visibility=2 color=200,0,200 useScore=1 db=hg18 chr4 56010000 56015000 cloneA 900 + chr4 56014000 56019000 cloneB 200 + chr4 56017000 56023000 cloneC 800 - chr4 56021000 56028000 cloneD 300 -

46. Copyright OpenHelix. No use or reproduction without express written consent46 Custom Tracks: Upload Track File Upload and View your Track (step 4) Upload File

47. Copyright OpenHelix. No use or reproduction without express written consent47 Custom Tracks: Upload File from Computer Documentation template Click to browse your computer to find file

48. Copyright OpenHelix. No use or reproduction without express written consent48 Custom Tracks: Submit Track Submit File

49. Copyright OpenHelix. No use or reproduction without express written consent49 Custom Tracks: Track Appears in Genome Browser Default view of custom track is “full” Default view of other tracks set Documentation

50. Copyright OpenHelix. No use or reproduction without express written consent50 Custom Tracks: Track Appears in Table Browser Custom Track also appears in Table Browser

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

52. Load Copyright OpenHelix. No use or reproduction without express written consent52 Track Hubs in Genome Browser Track Hubs

53. Copyright OpenHelix. No use or reproduction without express written consent53 Track Hubs in Table Browser Track Hubs Load User Guide

54. Copyright OpenHelix. No use or reproduction without express written consent54 Table Browser and Custom Tracks Agenda Table Browser Introduction Table Browser: Setup and filters Table Browser: Intersections Custom Tracks: Table Browser & User Generated Exercises UCSC Table Browser: http://genome.ucsc.edu/

55. Copyright OpenHelix. No use or reproduction without express written consent55