These are some Free Apps to Tease out the Sequencing Science. However it currently work only on windows. Apart from your Windows PC or Laptop, you will also need a Ubuntu Server access with Required softwares installed.
Setting up your Windows Laptop/PC
1) You will also need .NET installed on your computer. Its highly likely that .NET is already on your computer. The latest Windows comes pre-installed with .NET. Therefore try opening the software. If you get an error and don’t see the software window Download and install .NET.
2) You will need one more piece of software, That is the putty family of software. This software will connect your computer to the Server/Cloud. Please Download Putty family of software and install in on your windows machine.
Computational machines setup
You will also need High end server to process the data. Each App will require certain software’s to be installed on the server.
Setting up Analysis
You will need to ensure that individual softwares are installed and accessible on PATH. Details of sample info file and required software configuration will be mentioned with each App.
Once you have the Server configured up with the right software, you need to transfer the fastq files to your server. The data files should reach in the home folder. The free App wont be able to access data in sub-folders. Transfer the data using any of the FTP software e.g. Filezilla, winscp or use our Data Transfer App.
The Apps are a combination of Script Generators and Script Executer. The Script generators generates Scripts based on your sample info file and the Specifics of your project. You will have the full access to modify the script based on your requirements. This is one of our most innovative feature, giving basic users a chance to start with simple workflows and get results after few clicks, to them to lean advanced options and start playing with the script as they move on to there journey of becoming an advanced user. The software comes in small units. You only download what you need. Thats how they got there name as Apps.
This App will transfer your fastq files from your PC/Laptop to the Bioinformatics Server or Cloud. Alternatively you can use FileZilla, WINSCP or FTPBOX. All your fastqc files should be in Home Folder. More Details ……
This App is to be used after your have created the script file using the below Apps. This app will take your script file and execute it. The more relevent results and the progress of the analysis will come via email. Other intermediate files and information can be obtained by accessing the server using FileZilla, WINSCP or FTPBOX. More Details …..
Below are the Script Generator Apps. These Apps will generate script files, which can be modified based on your specifics and executed using Script Executing App.
This App uses Bowtie, Tophat and Cufflinks to obtain the expression values for your RNA-SEQ data. Once you launch the App, you can click the Help button to learn how to use it. More Details ……
This App uses Bowtie, Tophat and Cufflinks to obtain the expression values for your RNA-SEQ data. Once you launch the App, you can click the Help button to learn how to use it. More Details …..