the ucsc table browser & custom tracks advanced searching and discovery using the ucsc table...
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The UCSC Table Browser & Custom Tracks
Advanced searching and discovery using theUCSC Table Browser and Custom Tracks
Osvaldo Graña
CNIO Bioinformatics Unit
Materials prepared by:
Warren C Lathe, Ph.D.
Version 19b
Copyright OpenHelix. No use or reproduction without express written consent 2
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/
Copyright OpenHelix. No use or reproduction without express written consent 3
The Table Browser
http://genome.ucsc.edu/
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Genome Browser Database
Primary table: positions, names, etc.
UnderlyingDatabase(MySQL)
Auxiliary table: related data
visualize search & download
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UCSC Genome Browser Reference
Publication
Karolchik, et al.The UCSC Table Browser data retrieval tool. Nucl. Acids Res. 32(Suppl 1), D493-D496 (2004)
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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 7
Discovery using the Table Browser
McMurray, C. Mechanisms of trinucleotide repeat instability during human development. Nature Reviews Genetics 11: 786-99
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The Table Browser
Open browser
Open browser
http://genome.ucsc.edu/
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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.
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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.
Copyright OpenHelix. No use or reproduction without express written consent11
Table Browser: Describe Table
Describe table
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 consent12
Table Browser: Choose Region to Search
Choose Region to Search Define region
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Table Browser: Upload Locations to Search
Paste Upload
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Table Browser: Quick Summary of Expected Hits
Data Summary
Nearly 1 million simple
Repeats annotated in the
Human genome
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 15
Table Browser: Filter to Refine Search
Create Filter
Submit Filter
Delete wildcard “*” and type in
“CAG” (uppercase)
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Table Browser: Output Data
Output dataIn 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 17
Table Browser: Output Formats
Output formats
Text Fields
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Table Browser: Fasta Sequence Output
Sequence
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Table Browser: Database Format Outputs
Database
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Table Browser: Custom Track Output
Custom Track
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Table Browser: Hyperlinks Output
Hyperlinks
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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
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Table Browser: Output configuration
Fields
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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/
Copyright OpenHelix. No use or reproduction without express written consent 25
Table Browser: Intersecting Data
Find simple repeats (sequence = CAG)
within known genes and get hyperlinks.
Intersect
2nd Table
Any Overlap
Submit
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Table Browser: Intersecting Data Narrows Search
Summary
Filtered simple repeats
Filtered simple repeats, intersected (overlapping)
w/ known genes
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Table Browser: Get hyperlinks
get output
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Table Browser: Exploring the results
HTT, chr4: 307…
CAG
Q
ATN1, chr12: 704…
CAG
Q
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Table Browser: Exploring the results
RAI1
CAG
Q
DMPK
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Table Browser: Exploring the results
CAG
DMPK
Direction of transcription
CTG
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The Table Browser
McMurray, C. Mechanisms of trinucleotide repeat instability during human development. Nature Reviews Genetics 11: 786-99
Copyright OpenHelix. No use or reproduction without express written consent 32
Table Browser: Correlating Data Tables
Correlate 2 Datasets
Get Results
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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/
Copyright OpenHelix. No use or reproduction without express written consent 34
Custom Tracks: Table Browser Searches
Create Track
Get Output
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Custom Tracks: Name and Configure Track
Download track file to desktop
Name Track:SRepeatKGenes
Describe Track:Intersection …
In Genome Browser
Choose defaultview in browser
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Custom Tracks: Open Track in Genome Browser
Open Details
Compare
“…caused by anexpanded, unstable
trinucleotide repeat…”
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Custom Tracks: Track in Table Browser
Custom tracks also are available for filtering and intersections
on the Table Browser
Custom Tracks
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Custom Tracks: Manage Custom Tracks
Edit TrackGenome Browser
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Custom Tracks: User-generated Data in Track
Custom Track How-to
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Custom Tracks: Four Steps to Create Track
Four steps to create a custom trackFormat your dataDefine browser characteristicsDefine track characteristics Upload and view your trackAdd URL for annotation details (option)
http://genome.ucsc.edu/goldenPath/help/customTrack.html
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Custom Tracks: Format your Data
Format Your Data (step 1)
GFFGTFPSLBEDWIG
bigBEDbigWIG
Etc...
Browser Extensible Data
chr4 56010000 56015000 cloneA 900 +chr4 56014000 56019000 cloneB 200 +chr4 56017000 56023000 cloneC 800 -chr4 56021000 56028000 cloneD 300 -
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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 -
ChromosomeStart En
dName Score (shading)
Additional optional fields: Thick region, Item color, Number of blocks,size of blocks, start position of blocks
Strand
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Custom Tracks: Browser Characteristics
Define Genome Browser Characteristics (step 2)
browser position chr4:56010000-56030000browser pix 800browser hide allbrowser pack snp130browser full knownGene
Default Position
Default Image Width
Default Track View
Default Track View
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Custom Tracks: Track Characteristics
Define Track Characteristics (step 3)
Score on (1) or off (0)
Default ColorDefault track visibility0=hide
1=dense2=full
3=pack4=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.
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Custom Tracks: The Track File
Our Track:
browser position chr4:56010000-56030000browser pix 800browser hide allbrowser pack snp130browser full knownGenetrack name=clones description="Clones" visibility=2 color=200,0,200 useScore=1 db=hg18chr4 56010000 56015000 cloneA 900 +chr4 56014000 56019000 cloneB 200 +chr4 56017000 56023000 cloneC 800 -chr4 56021000 56028000 cloneD 300 -
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Custom Tracks: Upload Track File
Upload and View your Track (step 4)
Upload File
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Custom Tracks: Upload File from Computer
Documentation template
Click to browse yourcomputer to find file
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Custom Tracks: Submit Track
Submit File
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Custom Tracks: Track Appears in Genome Browser
Default view of custom track is “full”
Default viewof other tracks set
Documentation
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Custom Tracks: Track Appears in Table Browser
Custom Track alsoappears in
Table Browser
Custom Tracks
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Custom Tracks from Outside Sources
Contributed Track
Load
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Track Hubs in Genome Browser
Track Hubs
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Track Hubs in Table Browser
Track Hubs
Load
User Guide
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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/
Copyright OpenHelix. No use or reproduction without express written consent 55
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