fastmap tutorial. installation requirements computer with 2gb of ram java runtime environment (jre)...
TRANSCRIPT
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FastMap
Tutorial
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Installation Requirements
Computer with 2GB of RAM
JAVA Runtime Environment (JRE) 6 http://java.sun.com/javase/downloads/?
intcmp=1281
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How to launch FastMap
Unzip the FastMap.zip file anywhere
Executable files in the directory: FastMap.exe FastMap.bat FastMap.alt.bat
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How to launch FastMap
To launch the application: Double-click on FastMap.exe
If FastMap.exe doesn’t work: Double-click on FastMap.bat
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How to launch FastMap
If the application cannot be launch with FastMap.exe or FastMap.bat: Edit FastMap.alt.bat Put the path of the directory where
the JAVA 6 JRE is installed in the variable JAVA_HOME
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How to launch FastMapPut the path of the directory where the JAVA 6 JRE is installed in the variable JAVA_HOME
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Interface
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Interface
Menus
Tasks buttons
Genes List
Progress bar
Cancel task
buttons
Chart
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Association Plot
CorrelationValues
SNPs
Threshold levels
99%95%
50%
Chromosome Gene
90%
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Menu
File menu (short cut: Alt+F)Open and load a gene expression file (short cut : Alt+F then G or Ctrl+G)
Tasks buttons
Open and load a SNP file (short cut : Alt+F then N or Ctrl+N)Open and load a HapMap SNP File(short cut : Alt+F then H or Ctrl+H)Open and load Transposed PLINK file(short cut : Alt+F then R or Ctrl+R)Quit the application(short cut : Alt+F then Q or Ctrl+Q)
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Association menu (short cut: Alt+A)
Menu
Plot the Correlation or F-Statistic(short cut : Alt+A then P or Ctrl+P)Write the Correlation or F-Statistic into files(short cut : Alt+F then W or Ctrl+W)Save the plotted chart(short cut : Alt+F then C or Ctrl+C)Open the UCSC browser(short cut : Alt+F then U or Ctrl+U)Write LocusZoom ready chromosome data file(short cut : Alt+F then L or Ctrl+L)
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Menu
Tools menu (short cut: Alt+T)
Open the option window(short cut : Alt+A then O or Ctrl+O)
Open the SNP Similarity window
Open the SNP Analysis window
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Options window
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SNP similarity window
Allow two groups to be defined based on SNP similarity and to perform a mean or median subtraction on each group values for the correlation or F-statistic.
The checked strains form the first group and the unchecked strains form the second group.
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SNP similarity window
Example of two groups
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SNP similarity window
Example of two groups
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Input files
The application expects either: A gene expression file and SNP file
that are both tab delimited text files. Or a gene expression file and a tree
file which is a binary file produce by FastMap.
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Input files
All the strains that are in the gene expression file must be in the SNP file.
The strain order does not matter. The SNP file can contain more
strains than the gene expression file.
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Gene expression file
Fist line is the header
Microarray probe ID
Something more meaningful like the gene name
Strains Gene expression data
FastMap will display this
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SNP data fileStrains
Chromosome
Mb position SNP
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Select the association type
Set the association typeCorrelation: window size = 1F-Statistic: window size > 1Recommended size = 3
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Load the files
Open and load a gene expression file (short cut : Alt+F then G or Ctrl+G)
Tasks buttons
Open and load a SNP file (short cut : Alt+F then N or Ctrl+N)
The files can be loaded by using the menu or the buttons bar
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Plot a chart
Right-click on a gene name
Double-click on a gene name
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Association chart
Zoom in or out by using the mouse wheel or by selecting an area
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UCSC browserSend data to
UCSC browser if the current view is on a
single chromosome
.
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UCSC browser
FastMap track
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LocusZoom ready files
FastMap allows the user to write LocusZoom ready files to send results directly to LocusZoom, which will plot genes and SNP annotation in a specified region of interest.
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LocusZoom ready filesWrite
LocusZoom ready files.
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Write associations
Set the default output directory where the correlation or F-statistic files will be written
Set what output files will be written
Set writing options
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Write association
Right-click on a gene name
Several genes can be selected