Fig. 1

CANEapp and the graphical user interface. a General structure of CANEapp. The Java application component is the only user-accessible component and operates on a personal computer to provide a point and click interface to configure RNA-seq analysis. The interface either establishes a connection with an Amazon Cloud instance (1) created using the preconfigured CANEapp Amazon Machine Image (AMI) or with a Unix server, in which case server-side pipeline components are automatically transferred to the server through the GUI. After configuring a project, the GUI communicates with the server side to transfer raw data files and options file and initiate the analysis. b Design of the CANEapp’s graphical user interface. c CANEapp GUI’s capabilities and project design steps. The Manage Projects tab allows creating, deleting or loading projects from a file. Additionally, user can see the status of the selected project on this tab. The next two tabs allow adding experimental groups and samples. On the Add Samples tab the user can specify the library preparation that has been used before sequencing and define such parameters as single or paired-end sequencing, strand selection and adapter sequences. The Analysis Settings tab is used to set up parameters of separate analysis steps, such as alignment, reconstruction and differential expression analysis. Finally, the last tab is used to specify server address and user credentials and initiate the analysis on the server side