Copyright OpenHelix. No use or reproduction without express written consent 1 Important note to slide users: PC users Mac users a 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. Copyright OpenHelix. No use or reproduction without express written consent 2 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 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/ Copyright OpenHelix. No use or reproduction without express written consent 4 The Table Browser http://genome.ucsc.edu/ Copyright OpenHelix. No use or reproduction without express written consent 5 Genome Browser Database visualize search & download Underlying Database (MySQL) Primary table: positions, names, etc. Copyright OpenHelix. No use or reproduction without express written consent Auxiliary table: related data 6 UCSC Genome Browser credits http://genome.ucsc.edu/goldenPath/credits.html Open Credits Developers http://genome.ucsc.edu/staff.html Copyright OpenHelix. No use or reproduction without express written consent 7 UCSC Genome Browser credits License Copyright OpenHelix. No use or reproduction without express written consent 8 UCSC Genome Browser Reference Karolchik, et al. The UCSC Table Browser data retrieval tool. Nucl. Acids Res. 32(Suppl 1), D493-D496 (2004) Publication Copyright OpenHelix. No use or reproduction without express written consent 9 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/ Copyright OpenHelix. No use or reproduction without express written consent 10 The Table Browser Open browser Open browser http://genome.ucsc.edu/ Copyright OpenHelix. No use or reproduction without express written consent 11 Table Browser: Choose Genome 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. Copyright OpenHelix. No use or reproduction without express written consent 12 Table Browser: Choose Table to Search Choose Data Table Custom Tracks In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 13 Table Browser: Describe Table Describe table Copyright OpenHelix. No use or reproduction without express written consent 14 Table Browser: Choose Region to Search Choose Region to Search Define region In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 15 Table Browser: Upload Locations to Search Paste Upload Copyright OpenHelix. No use or reproduction without express written consent 16 Table Browser: Filter to Refine Search Create Filter Submit Filter In the Human genome, search for simple repeats on a chromosome 4 location with copy number more than 10 and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 17 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. Copyright OpenHelix. No use or reproduction without express written consent 18 Table Browser: Output Formats Text Fields Output formats Copyright OpenHelix. No use or reproduction without express written consent 19 Table Browser: Fasta Sequence Output Sequence Copyright OpenHelix. No use or reproduction without express written consent 20 Table Browser: Database Format Outputs Database Copyright OpenHelix. No use or reproduction without express written consent 21 Table Browser: Custom Track Output Custom Track Copyright OpenHelix. No use or reproduction without express written consent 22 Table Browser: Hyperlinks Output Hyperlinks Copyright OpenHelix. No use or reproduction without express written consent 23 Table Browser: Obtaining Output Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Data Summary Copyright OpenHelix. No use or reproduction without express written consent 24 Table Browser: Output configuration Sequence Format Get Sequence Copyright OpenHelix. No use or reproduction without express written consent 25 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/ Copyright OpenHelix. No use or reproduction without express written consent 26 Table Browser: Intersecting Data 2nd Table Any Overlap Intersect Submit Find simple repeats (copy number > 10) within known genes and download the sequence. Copyright OpenHelix. No use or reproduction without express written consent 27 Table Browser: Intersecting Data Narrows Search Filtered simple repeats Summary Filtered simple repeats, intersected (overlapping) w/ known genes Copyright OpenHelix. No use or reproduction without express written consent 28 Table Browser: Downloading Sequence Data Sequence Format Get Sequence Copyright OpenHelix. No use or reproduction without express written consent 29 Table Browser: Correlating Data Tables Get Results Correlate 2 Datasets Copyright OpenHelix. No use or reproduction without express written consent 30 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/ Copyright OpenHelix. No use or reproduction without express written consent 31 Custom Tracks: Table Browser Searches Create Track Copyright OpenHelix. No use or reproduction without express written consent 32 Custom Tracks: Name and Configure Track Name Track: SRepeatKGenes Describe Track: Intersection … Choose default view in browser Download track file to desktop Copyright OpenHelix. No use or reproduction without express written consent 33 Custom Tracks: Open Track in Genome Browser Open Details Compare “…caused by an expanded, unstable trinucleotide repeat…” Copyright OpenHelix. No use or reproduction without express written consent 34 Custom Tracks: Track in Table Browser Custom Tracks Custom tracks also are available for filtering and intersections on the Table Browser Copyright OpenHelix. No use or reproduction without express written consent 35 Custom Tracks: Manage Custom Tracks Genome Browser Edit Track Copyright OpenHelix. No use or reproduction without express written consent 36 Custom Tracks: User-generated Data in Track Custom Track How-to Custom Tracks Link Copyright OpenHelix. No use or reproduction without express written consent 37 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 Copyright OpenHelix. No use or reproduction without express written consent 38 Custom Tracks: Track Characteristics Define Track Characteristics (step 1) track name=pairedReads description="Clone Paired Reads" visibility=3 color=0,128,0 useScore=1 Default track visibility 0=hide 1=dense 2=full 3=pack 4=squish Default Color Score on (1) or off (0) Copyright OpenHelix. No use or reproduction without express written consent 39 Custom Tracks: Browser Characteristics Define Genome Browser Characteristics (step 2) Default Position browser position chr22:1000-10000 browser pix 620 browser hide all browser full gap Default Image Width Default Track View Default Track View Copyright OpenHelix. No use or reproduction without express written consent 40 Custom Tracks: Format your Data Format Your Data (step 3) Browser Extensible Data GFF GTF PSL BED WIG 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 Copyright OpenHelix. No use or reproduction without express written consent 41 Custom Tracks: Format your Data Browser Extensible Data Chromosome Start End Name Score Strand Thick Thick Color Blocks Block Block start end Sizes starts 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 Copyright OpenHelix. No use or reproduction without express written consent 42 Custom Tracks: Upload Track File Upload and View your Track (step 4) Upload File Copyright OpenHelix. No use or reproduction without express written consent 43 Custom Tracks: Upload File from Computer Click to browse your computer to find file Documentation template Copyright OpenHelix. No use or reproduction without express written consent 44 Custom Tracks: Submit Track Submit File Copy and paste small or simple tracks Copyright OpenHelix. No use or reproduction without express written consent 45 Custom Tracks: Track Appears in Genome Browser Copyright OpenHelix. No use or reproduction without express written consent 46 Custom Tracks: Track Characteristics Default view of custom track is “pack” Default view of other tracks set Copyright OpenHelix. No use or reproduction without express written consent 47 Custom Tracks: Track Appears in Table Browser Custom Track also appears in Table Browser Copyright OpenHelix. No use or reproduction without express written consent 48 Custom Tracks: Genome Graphs Genome Graphs Copyright OpenHelix. No use or reproduction without express written consent 49 Custom Tracks: Genome Graphs Browser Copyright OpenHelix. No use or reproduction without express written consent 50 Custom Tracks from Outside Sources Contributed Track Custom Tracks Copyright OpenHelix. No use or reproduction without express written consent 51 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/ Copyright OpenHelix. No use or reproduction without express written consent 52 The Table Browser Open browser Open browser http://genome.ucsc.edu/ Copyright OpenHelix. No use or reproduction without express written consent 53 Table Browser: Advanced Searching Genomes Data Location Filter and Intersect Output Copyright OpenHelix. No use or reproduction without express written consent 54 Custom Tracks: Table Browser Searches Create Track Copyright OpenHelix. No use or reproduction without express written consent 55 Custom Tracks: User-generated Data in Track Custom Track How-to Custom Tracks Link Copyright OpenHelix. No use or reproduction without express written consent 56 Additional UCSC Genome Tools Gene Sorter Proteome Browser In-Silico PCR VisiGene Copyright OpenHelix. No use or reproduction without express written consent 57 Contact Information and Mailing Lists Contact Info & Mailing Lists Copyright OpenHelix. No use or reproduction without express written consent 58 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 Copyright OpenHelix. No use or reproduction without express written consent 59 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/ Copyright OpenHelix. No use or reproduction without express written consent 60 Copyright OpenHelix. No use or reproduction without express written consent 61