FastMap

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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/?intcmp1281

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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 doesnt 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 FastMap
Put 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
Tasks buttons
Menus
Genes List
Chart
Cancel task buttons
Progress bar
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Association Plot
Threshold levels
Chromosome
Gene
99
95
90
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Correlation Values
SNPs
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Menu

• File menu (short cut AltF)

Open and load a gene expression file (short cut
AltF then G or CtrlG)
Open and load a SNP file (short cut AltF then
N or CtrlN)
Open and load a HapMap SNP File (short cut
AltF then H or CtrlH)
Open and load Transposed PLINK file (short cut
AltF then R or CtrlR)
Quit the application (short cut AltF then Q or
CtrlQ)
Tasks buttons
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Menu

• Association menu (short cut AltA)

Plot the Correlation or F-Statistic (short cut
AltA then P or CtrlP)
Write the Correlation or F-Statistic into
files (short cut AltF then W or CtrlW)
Save the plotted chart (short cut AltF then C
or CtrlC)
Open the UCSC browser (short cut AltF then U
or CtrlU)
Write LocusZoom ready chromosome data file (short
cut AltF then L or CtrlL)
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Menu

• Tools menu (short cut AltT)

Open the option window (short cut AltA then O
or CtrlO)
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
Something more meaningful like the gene name
Strains
Gene expression data
Microarray probe ID
Fist line is the header
FastMap will display this
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SNP data file
Strains
Chromosome
SNP
Mb position
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Select the association type
Set the association type Correlation window size
1 F-Statistic window size gt 1 Recommended size
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Load the files
The files can be loaded by using the menu or the
buttons bar
Open and load a gene expression file (short cut
AltF then G or CtrlG)
Open and load a SNP file (short cut AltF then
N or CtrlN)
Tasks buttons
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Plot a chart
Double-click on a gene name
Right-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 browser
Send 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 files
Write LocusZoom ready files.
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Write associations
Set writing options
Set the default output directory where the
correlation or F-statistic files will be written
Set what output files will be written
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Write association
Several genes can be selected
Right-click on a gene name