FAQ === Errors when starting SCOUTS --------------------------- **I can't start SCOUTS on my computer!** ``scouts`` **does nothing!** Please check the `installation troubleshooting section <./install.html#troubleshooting>`_. **I can't start SCOUTS-violins on my computer!** ``scouts-violins`` **does nothing!** Please confirm that you have installed the `necessary dependencies <./install.html#optional-scouts-violins>`_. Then check the `installation troubleshooting section <./install.html#troubleshooting>`_. About the SCOUTS workflow ------------------------- **What type of pre-processing does SCOUTS perform on my input?** By default, SCOUTS does not perform any pre-processing prior to analysing the input data. This means that transformations like data normalization and scaling should be performed by the user prior to using SCOUTS. SCOUTS does, however, include a simple module for gating mass cytometry and scRNA-seq samples, should the user want to do so. Refer to `How SCOUTS works <./howscoutsworks.html#gating-window>`_ for details. **My data is stored in multiple files. How do I use SCOUTS with it?** Ideally, you are able to merge your files into a single input file and use that to work with SCOUTS. When this is not possible, you can still use SCOUTS to run individual samples by passing one file at a time. This will not affect the output, *as long as all the cells from one sample are together in one file*. One side-effect of this method is that, in order to use the "*control*" option in the "*Consider outliers using cutoff from*" field, you need to make sure that the cells from the control sample are present in every file. **Does the output for non-outliers exclude both top and bottom outliers?** Yes. Even if you did not generate output files for bottom outliers, non-outliers are still considered as being "the population of cells that are not top outliers, nor bottom outliers". Misc. ----- **I have another question/suggestion/issue when using SCOUTS. How do I contact you?** You can contact us through our `Github page `_. Check the authors section for more information. Also remember that you can use the `Github issues `_ to post about problems or suggestions for SCOUTS. **SCOUTS is working nicely, but can you implement X?** Maybe! Tell us more about it on the `Github issues page `_ :-)