Mini-tutorials for common use-cases and to address frequently asked questions FAQs
After loading the sequences, the run blast icon is greyed out in OmicsBox, why? It is possible to load more than one project into OmicsBox and each project will be displayed in a different tab.So to run the analysis on the different projects you will need to have the OmicsBox table active (white tab). In your case, probably the Progress
It is possible to perform a Fisher Exact Test on the 2 groups even if the annotation is in different files (.annot). First, both .annot files (group 1 and group 2) need to be loaded into Blast2GO.The test and reference set have to be generated according to the groups you want to compare. These are normal text files with the
This article explains what a Gene Set Enrichment Analysis (GSEA) is, how it works and how to use it with OmicsBox. What is an enrichment analysis? Enrichment analyses are a family of bioinformatics methods that aim to facilitate the biological interpretation of many bioinformatics results. Among these, the methods based on gene sets analysis are particularly helpful and widespread. The
OmicsBox/Blast2GO automatically reserves up to 80% of the available system memory (i.e. RAM), which is fine in most cases. However, sometimes and especially on Linux, this can lead to excessive swapping and will slow down Blast2GO. Follow this guide to manually change the maximum amount of memory Blast2GO will be allowed to use.
OmicsBox/Blast2GO can handle big data, but it needs plenty of free disk space in the systems temporary files folder. If you run into troubles with a shortage of disk space, follow this guide to manually change the location of the folder for Blast2GO temporary files to e.g. another partition.
How to know if all your sequences have been analyzed The Analysis Progress chart is a very useful representation, which shows the step of the analysis in which the sequences in your dataset are found. They can be in different states, each represented by a color: Total: grey Without Analysis: white With IPS: purple With Blast Hits: orange Without Blast
(Show Blast Results, Welcome Part, Create Workflow) running Linux system. This applies to OmicsBox or Blast2GO 5. You need to install some packages depending on your distribution in order to make some parts work. For Ubuntu/Debian: apt-get install libxss1 libgconf-2-4 For Fedora: yum install libXScrnSaver libXScrnSaver.i686 GConf2 For CentOS: yum install libXScrnSaver GConf2 For more information on Show Blast Results
To the Blast2GO installer in Linux systems follow the next steps: 0. Open a terminal in the folder where you have downloaded the installer. 1. Unzip the file: tar -xvf Blast2GO_unix_X_X_XX.zip 2. Make sure the .sh file has execution permissions: chmod +x Blast2GO_unix_X_X_XX.sh 3. Execute the .sh file: ./Blast2GO_unix_X_X_XX.sh An installation wizard should open. Just follow the instructions on the
This article describes how you can get OmicsBox installed in a central computer where multiple users have access and what you need to configure so that it doesn’t ask for the License key for every new user and the updates are performed centrally. 0.0. You need a Unix user group that common to all the users that will execute OmicsBox.
