ENCODE UCSC data
Hello. I am interested in DNAse and ChIP seq signals from ENCODE UCSC tracks. For each experiment several types of data are available: Peaks, Hotspots, Raw Signals, Density Signal, Overlap Signal. I thought that choosing Peaks was a good thing, but in several cases it seems to me that they are too different from other types of data. Any suggestions? Please let me know. Cheers.
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The best data type will depend on what you plan to do with it... If you want to make heatmaps/meta-profiles then density signal or overlap signal is probably best. If you want to compare the overlap of various binding events then peaks.hotspots would be best. Hotspots are just peaks for DNase data (uses the hotspot algorithm).