HATSEQ consists five main buttons: * ‘Load Recent Setting’ * ‘Select Files’ * ‘Options’ * 'Additional Analysis’ * ‘Save and Analyze’. Three of these buttons are initially disabled. To get these buttons enabled, files have to be added first by clicking ‘Select Files’ button. At the bottom of this screen, there are two small buttons: * ‘info’ is the information screen * ‘quit’ is to close HATSEQ
Add Files screen
After clicking ‘Select Files’ button, user will have to select file to add to the ‘Add Files’ screen. Multiple files selection is allowed.
User can add new experiment by selecting one file on the left list and clicking ‘Experiment’ button. To add a file as control to an experiment, just select that file on the left list and the experiment on the right list, then click the ‘Control’ button. As an example in Figure 2, STAT1 has been added as an experiment, while unstimulated has been added as its control. These experiments can be deleted using ‘Delete Analysis’ button. When you are done, just click the ‘OK’ button. This screen will disappear and the HATSEQ home screen will show up, but this time, all buttons will be enabled. At this moment, user can start the analysis by clicking on ‘Save and Analyze’ button, but there are two extra options available, ‘Options’ and ‘Additional Analysis’.
In the "options" screen, there are several options that can be set:
1. Email (optional) 2. Alpha Default = 0.05 3. Common region of interest If ‘Yes’ is checked, then this Common ROI among samples screen will show up 4. Fragment size Default = 300
Additional Analysis screen
In the "additional analyses" screen, there are several options that can be set:
1. Save figure Default = ‘.png’. 2. Gene mapping If ‘Yes’ is checked, then a new screen will show up with a list of species from UCSC Genome Browser website. 3. Pathway analysis This option will only be available when gene mapping is checked. If ‘Yes’ is checked, then pathway analysis screen shows up with several options. a. Alpha b. Multipletest c. Gene sets 4. FASTA files This option works almost the same as Gene Mapping option. If ‘Yes’ is checked, then a new screen will show up with a list of species from UCSC Genome Browser website. 5. Motif analysis This option works similar to Pathway analysis. It becomes available when FASTA files is checked. If ‘Yes is checked, then motif analysis screen shows up with several options. a. Alpha b. Multipletest c. Analyze both strands d. Sequence of interest 6. UCSC custom track Default = ‘No’.
For Gene mapping and FASTA files: When a gene mapping file or a chromosome directory of a species does not exist yet, the user will be asked if he/she wants to download them or to select his/her own gene mapping file or chromosome directory.