There are three scatter plots. You can first choose the data you want to use for X-axis and Y-axis in each plot using the dropdown tool. Then you can choose whether to use the raw signal value or the percentiles of values. To interactively explore the plots, you can try clicking and dragging in any of the plots to filter different regions. Notably, only the intersection of the selections from three plots will be highlighted with a different color. For example, you can select a region on the first plot. The selected points will be highlighted in all three plots. Then, you can further select a subset of points in the second and third plots. To remove a selection for a plot, you can double click at any position in that plot or draw a selection without any points. Finally, you can download the highlighted regions are a bed file by clicking the DOWNLOAD button. A dialog will pop up showing you how many regions are exported.
To use your data, you should firstly prepare a TSV file (i.e., columns are separated by tabs). The first row is the column name. We recommend you to prepare data in bed format with the first three columns as chromosome, start position, and end position. The rest columns can be functional readouts. 'NA' values may cause some problems, so please remove any rows with 'NA' values. Once you upload a new file, the dropdown tool should automatically update to list the available columns that you can choose.