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 FastMapPut the path of the directory where the JAVA 6 JRE is installed in the variable JAVA_HOME

Interface

Interface

Menus

Tasks buttons

Genes List

Progress bar

Cancel task

buttons

Chart

Association Plot

CorrelationValues

SNPs

Threshold levels

99%95%

50%

Chromosome Gene

90%

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)

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)

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

Fist line is the header

Microarray probe ID

Something more meaningful like the gene name

Strains Gene expression data

FastMap will display this

SNP data fileStrains

Chromosome

Mb position SNP

Select the association type

Set the association typeCorrelation: window size = 1F-Statistic: window size > 1Recommended size = 3

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

Plot a chart

Right-click on a gene name

Double-click on a gene name

Association chart

Zoom in or out by using the mouse wheel or by selecting an area

UCSC browserSend 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 filesWrite

LocusZoom ready files.

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

Write association

Right-click on a gene name

Several genes can be selected