User Interface

See Figure 4 for the explanation of the GUI of TSSpredator.

Study setup In the study setup area (Figure 4 A) general settings for the study can be made. Most importantly these are the type of the study (comparison of strains (requires alignment file) or conditions), the number of genomes/conditions and replicates, and the path to the output directory. A project name can also be specified.

Parameter area In the parameter area (Figure 4 B) specific parameters of the TSS prediction procedure can be changed. Instead of changing individual parameters it is also possible to select a parameter preset from the drop-down menu.

Genome/Condition related settings For each genome/condition of the study a tab is generated (Figure 4 C), in which settings specific for this genome/condition can be made. This includes the name and ID, and file paths to the genomic sequence (FASTA) and the genome annotation (GFF). In addition, for each replicate a tab is displayed within the respective genome/condition tab, where the RNA-seq wiggle files of the replicate can be entered. If only fastq files are available instead of wiggle files, it is recommended to use the READemption pipeline (see section READemption to generate them).

Message Area In the message area (Figure 4 D) information about a running prediction process is displayed. Thus, it can be easily determined in which step a running prediction procedure currently is. At the end of the procedure a brief summary is shown.

Load/Save Configuration Using the Save or Load button (Figure 4 E) a configuration including all settings can be saved, or a previously saved configuration can be loaded, respectively. Loading a configuration overwrites all current settings.

Run prediction By pressing the RUN button (Figure 4 F) the prediction procedure is started using the current settings and parameters. Information about the running process is displayed in the message area. The running prediction can be canceled using the Cancel button. Note that this might result in incomplete output files.