The HMC scores were downloaded and converted to .bedGraph files with a custom Python script. The bedGraph files were then converted to bigWig files, as documented in our makeDoc hg19 build log.
MTR data can be found on two tracks, MTR All data and MTR Scores. In the MTR Scores track the data has been converted into 4 separate signal tracks representing each base pair mutation, with the lowest possible score represented when -multiple transcripts overlap. It is recommended that the data be explored using +multiple transcripts overlap. A horizontal line is drawn on the 0.8 score line +to roughly represent the 25th percentile, meaning the items below may be of particular +interest. It is recommended that the data be explored using this version of the track, as it condenses the information substatially while retaining the magnitude of the data.
Any specific point mutations of interest can then be researched in the MTR All data track. This track contains all of the information from MTRV2 including more than 3 possible scores per base when transcripts overlap. A mouse-over on this track shows the ref and alt allele, as well as the MTR score and the MTR score percentile. Filters are available for MTR score, False Discovery Rate (FDR), MTR percentile, and variant consequence. By default, only items in the bottom 25 percentile are shown. Items in the track are colored according to their MTR percentile: