Thank you for your question about the differences of the of DNaseI Hypersensitivity Clusters and DNaseI Hypersensitive Site Master List tracks in the UCSC Genome Browser.
Below are links to the Track Description pages for each track where you can read more detailed information about these data:
Here is a session loading the two tracks around a gene, SIRT1:http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Brian%20Lee&hgS_otherUserSessionName=hg19.SIRT1.DNase
Your original thinking is correct, the clusters track provides another view of the masters sites track. Reading the descriptions you will learn the clusters track is a version of the same data, where the master site list was clustered, by UCSC with a program called regCluster, and where low-scoring clusters (score <100) were filtered out. Thus there will be some discrepancies between the two tracks. Some of the master sites will failed to cluster into groups that met the minimum score threshold, and hence are missing from the clusters track. If the clustering and filtering features of the DNaseI Hypersensitivity Clusters track are undesirable, the masters list provides a chance to see a less processed level of the data.
Also, just in case you have previously viewed the wgEncodeRegDnaseClustered, under the Release Notes, you will find an explanation that this is the third version of the track. There was a previous V2 version, located now only on genome-preview, http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegDnaseClusteredV2
, where the clustering program was limiting clusters to only those that had at least two cell types.
Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu
. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu
All the best,
UCSC Genome Bioinformatics Group