Table Browser and Custom Tracks

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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
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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
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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
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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
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22
Table Browser: Hyperlinks Output
Hyperlinks
Copyright OpenHelix. No use or reproduction without express written consent
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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
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
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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

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
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
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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
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57
Contact Information and Mailing Lists
Contact Info & Mailing Lists
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58
Additional Materials available: www.openhelix.com

UCSC sponsored material at www.openhelix.com/ucsc
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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
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