AltAnalyze runs best on a machine with a 64bit operating system and at least 8GB of RAM. It can work with less RAM, however, Kallisto FASTQ file pseudoalignment may not run on all operating systems with less than 8GB of RAM.
Downloading and Extracting AltAnalyze
AltAnalyze can be downloaded as a zip or DMG file from SourceForge or the AltAnalyze website. If running the command-line version on a linux machine or remote server/cluster, we recommend installing AltAnalyze directly from GitHub as described here. For most users, installing the Windows or Mac compiled version will be easiest, as these versions have all dependencies included. Once downloaded, you can extract to your desired Application directory using a standard zip extraction tool, such as WinZip or WinRAR (Windows). Mac DMG files can easily be opened by double-clicking on the DMG file.
Installing the Species Database
As shown in this video, the primary AltAnalyze species database or databases can be easily installed through the graphical user interface. The user will be prompted to install such a database when first double-clicking on the AltAnalyze executable (AltAnalyze application folder, AltAnalyze or AltAnalyze.exe file). Alternatively, if installing the command-line version, see the instructions here. You must have an active web-connection to install. Three main options are present in the GUI installation window: 1. Database version to select 2. Species to select 3. Download/update all gene-set analysis databases
AltAnlayze supports different genome builds for the 60+ supported species. Different genome builds correspond to different versions of the (Ensembl database)[http://www.ensembl.org]. If you already have aligned sequence results (e.g., BAM files), you need to download the appropriate matched genome version that your data was aligned to in order for AltAnalyze to figure out how to analyze your data. With FASTQ files, AltAnalyze will align the sequences to the database and genome version you download here. You can go to Ensembl and see what versions are supported for each database. For example, EnsMart72 corresponds to hg19 for human and mm10 for mouse. To see this at Ensembl go to this following FTP link (the genome version is indicated for the species of interest as the last number in the folder name). Different database versions in AltAnalyze may support different species.
After selecting your species of interest, you can choose to select or de-select the Download/update all gene-set option. De-selecting for mouse and human will save time, as most all accessory databases are up-to-date. Select continue to download. The download can take up-to 30 minutes depending on the access speed.
Installing the RNA-Seq Database
If you are processing primary RNA-Seq data files (e.g., FASTQ, BAM, junction.bed, TCGA), you need to additionally install a second database. If you are only analyzing existing normalized gene expression files, you don't have to download the RNA-Seq database as requirement. Instead, select Other as your "Vendor/Data Type" from the Main Menu and the gene or protein ID system in the first column for your input text file from the "Select Platform" option. To download the RNA-Seq database, simply select RNASeq from the "Vendor/Data Type" Main Menu option, your species of interest (if multiple present) and Continue. AltAnalyze will automatically download this database (5-30 minutes). At this point you are ready to analyze your data. Contact us to assist with any problems at our Google Groups.