Download FastMap

FastMap
Tutorial
Installation Requirements

Computer with 2GB of RAM

JAVA Runtime Environment (JRE) 6

http://java.sun.com/javase/downloads/?intcmp
=1281
How to launch FastMap

Unzip the FastMap.zip file anywhere

Executable files in the directory:



FastMap.exe
FastMap.bat
FastMap.alt.bat
How to launch FastMap

To launch the application:


Double-click on FastMap.exe
If FastMap.exe doesn’t work:

Double-click on FastMap.bat
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
How to launch FastMap
Put the path of the directory where the JAVA 6 JRE is installed in
the variable JAVA_HOME
Interface
Interface
Menus
Tasks
buttons
Genes
List
Chart
Cancel task
buttons
Progress
bar
Association Plot
Chromosome
Gene
Threshold
levels
99%
95%
90%
50%
Correlation
Values
SNPs
Menu

File menu (short cut: Alt+F)
Open and load a gene expression file
(short cut : Alt+F then G or Ctrl+G)
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)
Tasks buttons
Menu

Association menu (short cut: Alt+A)
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)
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
Options window
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.
SNP similarity window
Example of
two groups
SNP similarity window
Example of
two groups
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.
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.
Gene expression file
Microarray probe ID
Fist line is
the header
FastMap will
display this
Something more meaningful
like the gene name
Strains
Gene expression data
SNP data file
Strains
Chromosome
Mb position
SNP
Select the association type
Set the association type
Correlation: window size = 1
F-Statistic: window size > 1
Recommended size = 3
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 : Alt+F then G or Ctrl+G)
Open and load a SNP file
(short cut : Alt+F then N or Ctrl+N)
Tasks buttons
Plot a chart
Double-click on
a gene name
Right-click on a
gene name
Association chart
Zoom in or out by
using the mouse
wheel or by
selecting an area
UCSC browser
Send data to
UCSC browser
if the current
view is on a
single
chromosome.
UCSC browser
FastMap track
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.
LocusZoom ready files
Write
LocusZoom
ready files.
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
Write association
Several genes
can be selected
Right-click on a
gene name