Download presentation UCSC part 2 - Biomedical Genomics Group

The Genome
Genome Browser Training
Part 2
Materials developed by:
Warren C. Lathe, Ph.D. and Mary Mangan, Ph.D.
[email protected]
Gene Sorter
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Basic searches using the Genome Browser
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Text searching, Sequence Searching (BLAT)
In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter
Advanced searching using the Table Browser
Custom Tracks
Hands-on session for Sorter, Table Browser, and Custom
Tracks
Gene Sorter
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From homepage select ‘Gene sorter’
Gene Sorter interface
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Sorts genes by several criteria
Gene Sorter interface
Choose genome
Choose assembly
Type in gene name
or accession #
Gene Sorter interface
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Choose from 11 sorting options
Gene Sorter interface
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Configure display view
Gene Sorter interface
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Filter data by different criteria
Gene Sorter results
Gene Sorter results
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Obtain file of gene sequences or tab-delineated file of data
Table Browser
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Basic searches using the Genome Browser
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Text searching, Sequence Searching (BLAT)
In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter
Advanced searching using the Table Browser
Custom Tracks
Hands-on session for Sorter, Table Browser, and Custom
Tracks
The Table Browser
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Download sequence of all simple repeats of copy number
more than 10 from a position on chromosome 4.
The Table Browser
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From the Genome Browser home page, select Table Browser
Table browser: choose genome
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Choose genome and assembly
Table browser: choose table to search
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Data tables are organized by group & annotation track.
Table browser: choose region to search
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Choose entire genome, ENCODE regions, enter a single
position
or alternatively paste or upload a file of positions.
Table browser: filter to refine search
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Filter is a form based sql query. Filters can be created for
primary table and for related tables
Table browser: Output formats
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Get fields of table data
Table browser: Output formats
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Fasta file of sequence data
Table browser: Output formats
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GTF or BED formated file
Table browser: Output formats
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Custom track
Table browser: Obtaining output
Adding name creates file on desktop,
leaving blank creates output in browser.
(exception: custom track)
Obtain a summary
of specified data
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Output as file or in browser.
Also, obtain statistics.
Table browser: Output configuration
The Table Browser
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Find simple repeats (copy number > 10) within known
genes and download the sequence.
Table browser: Intersecting data
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Intersect table with another table of data
Table browser: Intersecting data
Filtered simple repeats
Filtered simple repeats,
intersected (overlapping)
w/ known genes
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Obtaining summary shows how intersecting narrowed search
Table browser: Intersecting data
Table browser: Correlating data
Custom Tracks
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Basic searches using the Genome Browser
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Text searching, Sequence Searching (BLAT)
In Silico PCR, Proteome Browser
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Hands-on session for Basic Searches
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Gene Sorting search using the Gene Sorter
Advanced Searching using the Table Browser
Custom Tracks
Hands-on session for Sorter, Table Browser and Custom
Tracks
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Custom Tracks
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Custom Tracks
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Table Browser Searches
User-generated Data
Externally Generated Data
Custom Tracks: Table browser searches
Custom Tracks: Table browser searches
Custom Tracks: Table browser searches
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Custom Tracks can be viewed in the Genome Browser
Custom Tracks: Table browser searches
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Custom tracks also are available for filtering and
intersections on the Table Browser.
Custom Tracks: Table browser searches
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Intersecting previously created custom track finds one simple
repeat with copy number >10 in known genes that also
overlaps a CpG island.
Custom Tracks: Table browser searches
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Intersecting custom tracks with available data (or other
custom tracks) can be a powerful discovery tool.
Custom Tracks
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Custom Tracks
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Table Browser Searches
User-generated Data
Externally Generated Data
Custom Tracks: User-generated Data
Custom Tracks: User-generated Data
Custom Tracks
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Custom Tracks
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Table Browser Searches
User-generated Data
Externally Generated Data
Custom Tracks from Outside Sources
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Custom tracks list shared by the community
Hands-on Session
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Basic searches using the Genome Browser
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Text searching, Sequence Searching (BLAT)
In Silico PCR, Proteome Browser
Hands-on session for Basic Searches
Gene Sorting search using the Gene Sorter
Advanced searching using the Table Browser
Custom Tracks
Hands-on session for Sorter, Table Browser, and Custom
Tracks