In the latest Ensembl release (Ensembl 90, August 2017), we have added the option for you to adjust the y-axis of your custom “wiggle” tracks, such as BigWig and bedGraph files.
You can now choose the track parameters when uploading a BigWig or bedGraph file as a custom track, meaning that you can select the colour of the graph and normalise the y-axis on the custom tracks. Previously, automatic scaling adjusted the y-axis to the maxiumum value, making the plotting of noise vs. signal problematic and confusing. We hope that this feature will make it easier for data interpretation,for example ChIP-seq or RNA-seq experiments.
You can select the parameters of your custom track either when uploading the data file itself, or later on when viewing the custom data track.
When you attach a BigWig or bedGraph file, you will have the option to set the colour as well as the minimum and maximum values for the y-axis of the graph (see below). Simply select your colour of choice from the drop-down menu and enter the minimum and maximum values for the y-axis in the ‘Range Minimum’ and ‘Range Maximum’ fields, respectively. Alternatively, you can leave these fields blank, in which case automatic scaling will be performed for your custom data track.
Once the track is displayed, you can change the values by clicking on the track name in the left-hand edge of the region view and using the popup menu – the tab is marked by a histogram icon. You are then prompted to input the minimum and maximum y-axis values. Again, you can leave these fields blank to revert to automatic scaling for your custom data track. After you have selected your parameters, click on the ‘Update’ button or close the pop-up window and your custom track will be re-calibrated.
In the example below, you can see data from a ChIP-seq experiment (Track A) and the input control (Track B). In the top image, auto-scaling has adjusted the maximum y-axis value for each track separately, making the ChIP-seq and control track identical in height, despite the difference in signal (which you can see by the scale next to the track name). In the bottom image, taken from the new Ensembl release, the y-axis of the control track (B) has been adjusted to match the ChIP-seq data track (A). Now the difference between experimental and control tracks is much more visible.
With this new feature it’s important to remember that manual altering of maximum and minimum y-axis values may conceal data where, for example, large peaks are cut off by a small y-axis maximum value.