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Source code Current version: 1.17 User Manual: ALEXA-Seq_Manual_v.1.17.pdf Linux Installation Manual: ALEXA-Seq_LinuxInstall_v.1.17.pdf Change Log: CHANGELOG.txt Tarball Download directly from here: ALEXA_Seq_v.1.17.tar.gz SourceForge You can also obtain the current version (as well as old versions) from SourceForge.net: ALEXA-Seq at SourceForge Subversion If you have svn installed, you can checkout the code directly from our subversion repository. For example: cd /home/user/ svn checkout https://svn.bcgsc.ca/public/ALEXA_Seq/tags/ALEXA_Seq_v.1.17/ alexa_seq Virtual Machines Finally, you can download the code installed into a VMware Virtual Machine (VM). These VMs include the source code and all dependencies and tools needed for the analysis. The VM can be booted from a Mac, Windows or Linux desktop. It will run as a self-contained 'guest' operating system within a window on your 'host' system. To use the VM you will need to download and install a VMware player. There are several free options, or you can buy VMWare workstation (for Windows/Linux) or VMware Fusion (for Mac). Using the player, you can configure the number of CPUs and amount of memory used by the Virtual Machine. In addition to the player, the VM will run on the following VMware platforms: ACE, ESX, Fusion, Server, and Workstation. Furthermore, these VMs are compatible with public and private 'Cloud' computing services: vCloud, vSphere, vCenter. Our VMs were created and tested with VMware Workstation 7.1 on a Windows XP system with 2 CPUs and 4 Gb of memory (2.5 Gb available to the VM). They can be configured to use up to 8 CPUs/Cores, 32 Gb of memory, and 2 Tb of disk space from the host system. Virtual Machine Players (links to external websites open in a new window or tab): VMware Player (free): For Windows | For Linux VMware Fusion (free 30 day trial): For Mac VMware Workstation (free 30 day trial): For Windows or Linux ALEXA-Seq Virtual Machine Downloads: For 32-bit Host: ALEXA-Seq 32-bit v.1.12b.tar.gz (1.8 Gb) | ALEXA-Seq 32-bit v.1.12b.zip (1.8 Gb) For 64-bit Host: ALEXA-Seq 64-bit v.1.12b.tar.gz (1.9 Gb) | ALEXA-Seq 64-bit v.1.12b.zip (1.9 Gb) Note: This latest version of the VM (v.1.12) incorporates many performance improvements and a more simplified process for running the demonstration analysis. It has been tested successfully from start to finish on a Windows XP machine with 2Gb of memory allocated to the VM. Note: You must select the version that matches your CPU(s). Unless your computer is more than 2-3 years old it is very likely to be 64-bit. If you select the wrong version it may fail to boot properly. For a brief visual introduction to the VM, check out some screenshots or the slideshow Step by step instructions: 1.) Download and install one of the player options described above (the following assumes VMware player) 2.) Download the ALEXA-Seq virtual machine. Pick the 32-bit or 64-bit to match your system 3.) Unpack the archive. Use 'tar -zxvf ArchiveName.tar.gz' for Linux or Mac and 7-Zip for Windows. 4.) Start VMware player and select 'Open Virtual Machine' from the 'File' menu. 5.) Browse to where you unpacked the ALEXA-Seq VM, select 'ALEXA-Seq XX-bit.vmx', and select 'Open'. 6.) Select 'Edit virtual machine settings' to modify the number of CPUs and amount of memory used. 7.) When ready, select 'Play virtual machine'. The system will now boot inside a window. 8.) To toggle full screen mode press: 'Ctrl+Alt+Enter'. 9.) See the user manual for username and password: ALEXA-Seq_Manual_v.1.17.pdf 10.) If the screen resolution does not seem correct, adjust it: System -> Preferences -> Screen Resolution 11.) Open the file 'DEMO.txt' on the desktop for a demonstration. Virtual Machine Demonstration and System Requirements: The demonstration described in DEMO.txt involves analyzing a test dataset of several million paired reads (~4 million 2x42-mers) corresponding to MIP101 and MIP/5FU human colorectal cancer cell lines. The purpose of this demostration is to illustrate the analysis steps on a small dataset that can be analyzed quickly on a modest system. The analysis requires alignment to human reference genome sequences and involves the creation of large temporary files. Your system should have 20-30 Gb of free disk space. Since the VM is self-contained, when you are done testing, simply delete the directory containing the VM to free this disk space. We tested the VM demonstration on several Windows and Mac computers. Using 2 CPUs and 2 Gb of memory the demonstration analysis should complete is less than 24 hours. Database Schema To assist in the identification of alternative expression events by massively parallel RNA sequence data, we developed the 'ALEXA-Seq' annotation database. Briefly, this database defines expression ‘features’ that can be informative of alternative expression events such as exon skipping, alternative exon boundary usage, inclusion of cryptic exons, intron retention, etc. For the human genome (build 36 / hg18), a total of ~3.8 million such features were defined. Each feature was annotated with information describing its size, repeat content, protein coding content, mRNA/EST sequence support, cross-species conservation (by examining EST/mRNA alignments from other species), etc. and assigned a descriptive feature name. A detailed description of the values defined for each feature can be downloaded: ALEXA Seq Schema Description. For further details refer to Griffith et al.. Download a database for your species of interest or request a custom database below. ALEXA-Seq annotation databases available for download ALEXA_dm_54_54b (Fly)
ALEXA_dr_57_8c (ZebraFish)
ALEXA_gg_54_2l (Chicken)
ALEXA_hs_53_36o (Human - build36/hg18)
ALEXA_hs_55_37 (Human - build37/hg19)
ALEXA_hs_57_37b (Human - build37/hg19)
ALEXA_hs_60_37e (Human - build37/hg19)
ALEXA_hs_65_37j (Human - build37/hg19)
ALEXA_mm_54_37g (Mouse)
ALEXA_mm_60_37m (Mouse)
ALEXA_mm_65_37r (Mouse)
ALEXA_pt_54_21k (Chimp)
ALEXA_rn_54_34v (Rat)
ALEXA_sc_54_li (Yeast)
Request an additional species or other custom annotation database If you are interested in a particular species that is not included in the list above, you can download the source code and create it yourself. Or you can request the we generate it for your by contacting us. By default we create the exon-exon junction sequences with a length of 62 bases (suitable for 36 mer or greater reads). Before making a request, please first read the database schema description above to determine if the database would be useful for your analysis. Also, we are limited to species annotated by EnsEMBL (current list of EnsEMBL species: here). Acknowledgements Each species image above links directly to EnsEMBL. These images were obtained from www.ensembl.org |
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