.. |start| image:: ../../gui/img/Next.gif :alt: Start Run .. |stop| image:: ../../gui/img/Stop.gif :alt: Stop Run .. _quick: Quick Start Guide ================== This will guide the user through the process of using Xpression, at a rapid pace. For more detailed guidance, please see :ref:`install` and :ref:`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 :ref:`guide`. Obtain Xpression ^^^^^^^^^^^^^^^^^ Download `Xpression GUI `_ to your harddrive. Get the dataset ^^^^^^^^^^^^^^^^ Right click on `example dataset `_, select 'Save-as' to download the file to your harddrive. Right-click or double click this file to bring up an application to unpack this compressesed 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. .. figure:: ../../gui/img/main.png :alt: Main window of Xpression :align: center 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| *Start Run* button in the upper-right corner. This button will now change to |stop| *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| *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``.