1) Currently, the GUI only permits to use the default region sets. For including the 200bp you would have to turn to the script-based workflow. Thanks for the hint, we’ll think about how to make this easier by just using the GUI and add it to our "to-implement" list.
2) Currently, the GUI also does not directly provide to option to conduct paired analysis. However it can be tricked ;-)
To do so, set all the analysis options like you want them, except for the pairing part. Then export the options to XML using the “Save to XML” button in the Analysis Options tab of the GUI. Then, you can edit the XML file manually and specify the pairing like you would do in an R seession/script. For details on how to do this step, see the Answer to the the FAQ “How do I tell RnBeads to perform a paired test in the differential analysis module?” on our website (https://rnbeads.org/faq.html
). Afterwards, you can load the modified XML file again into the GUI using the “Load from XML” button. We'll make this easier in the future.
Hope that helps.