Quick Start Guide

This will guide the user through the process of using Xpression, at a rapid pace.

For more detailed guidance, please see Installation and Xpression user guide.

What you will need

• A graphical Linux system, supporting software, and Xpression GUI

  or

• The graphical virtual Linux system, Xpression VE

• The Example Dataset or your own data, including:

  • fastq sequencing file
  • fasta genome reference file
  • Genbank reference file

  The genome and Genbank reference files may be found from sources such as NCBI http://www.ncbi.nlm.nih.gov/nuccore or JGI http://img.jgi.doe.gov/cgi-bin/w/main.cgi.

Procedure

A sample sequencing file will now be analysed using Xpression. Each step is explained in further detail in Xpression user guide.

Obtain Xpression

Download Xpression GUI to your harddrive.

Get the dataset

Download the dataset from Example Dataset and uncompress this file to a convenient directory. Three files are packed inside: CGA009.fasta, CGA009.gbwithparts, and example.fastq.bz2. The fastq file is compressed and can be used as-is to conserve space.

Start Xpression

Start the Xpression application by double-clicking the Xpresson.jar from a where it was downloaded.

empty main window

Enter sample-specific information

In the Sample Details area, enter the barcode sequence of ACCC into the barcode field, and the name Example1 into the Sample ID field.

Define reference files

In the Sample References area, there are fields for each of the three required reference files.

For each of these three reference files, do the following:

• Click the left-hand button to open a file selection window. Locate and select the appropriate file from the example dataset package where it was decompressed on your computer.

Begin analysis

Click the Start Run button in the upper-right corner. This button will now change to Stop Run, to allow processing to be cancelled. Two windows will become visible, a run list and an Xpression output log window.

Explore results

Once Xpression analysis is finished, the upper-right button will change back to Start Run and the status in the run list will change from running to complete. The processed files are located at the output directory in the folder labelled by the sample ID.

In this case this will be your home folder > Xpression_results > example > Example1, since output directory is your_home_directory/Xpression_results, the sequence filename is example.fastq.bz2, and the sample ID is Example1.