Hi Peng, There is more information about hotspots vs. peaks on the track description pages. For the track you were referring to:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeUwDnase: Under "Display Conventions and Configuration": HotSpots: DNaseI sensitive zones identified using the HotSpot algorithm. Peaks: DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones. Under "Methods": DNaseI sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm (I-max). Regarding the difference between narrowPeak and broadPeak file formats: if a file is narrowPeak but does not use the final column, it is likely that the file could have just as easily been submitted to us by the data contributor as a broadPeak file. We do not enforce a requirement that narrowPeak files use the final column. If you are wondering about a particular narrowPeak file, you can contact the data contributor directly to find out why they chose to submit it as a narrowPeak (the contact information is in the track description. If you have further questions for us, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 6/7/12 8:54 AM, Peng Yu wrote: > Hi, > > It seems that the only difference between narrowPeak and broadPeak is > that narrowPeak has an additional (last) field, called "peak". > > narrowPeak: http://genome.ucsc.edu/FAQ/FAQformat#format12 > broadPeak: http://genome.ucsc.edu/FAQ/FAQformat#format13 > > However, this last field seems not used in at least some encode > narrowPeak files that I checked. > > ==> wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1.broadPeak.gz<== > chr1 3110517 3110671 . 0 . 5.448090 4.38084 -1 > chr1 3111585 3111623 . 0 . 3.671480 2.51999 -1 > chr1 3195954 3196070 . 0 . 2.369560 1.47742 -1 > chr1 3206152 3206391 . 0 . 3.071120 2.06238 -1 > chr1 3241950 3242270 . 0 . 6.636570 5.75176 -1 > chr1 3242593 3242899 . 0 . 5.051660 3.92101 -1 > chr1 3276435 3276459 . 0 . 2.369560 1.47742 -1 > chr1 3282816 3282924 . 0 . 3.935830 2.80068 -1 > chr1 3291106 3291285 . 0 . 2.476880 1.58953 -1 > chr1 3311646 3311805 . 0 . 3.736570 2.63924 -1 > > ==> wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1.narrowPeak.gz<== > chr1 3110500 3110650 . 0 . 11 4.38084 -1 -1 > chr1 3242020 3242170 . 0 . 11 5.75176 -1 -1 > chr1 3242680 3242830 . 0 . 8 3.92101 -1 -1 > chr1 3323840 3323990 . 0 . 16 8.02211 -1 -1 > chr1 3351080 3351230 . 0 . 34 26.4912 -1 -1 > chr1 3359740 3359890 . 0 . 38 35.735 -1 -1 > chr1 3385700 3385850 . 0 . 13 7.23909 -1 -1 > chr1 3389140 3389290 . 0 . 23 19.0234 -1 -1 > chr1 3406260 3406410 . 0 . 26 20.0498 -1 -1 > chr1 3437540 3437690 . 0 . 26 25.386 -1 -1 > > > According to the following description, the difference is "Hotspots" > vs "Peaks". But I'm not clear what is the difference between Hotspots > and Peaks. > > Could anybody clarify a bit on the differences between the two file > formats and between Hotspots and Peaks? > > +-------------------------------------------------------+-----------------+------------------------------------------------------------------+------------+ > | tableName | shortLabel > | longLabel > | grp | > +-------------------------------------------------------+-----------------+------------------------------------------------------------------+------------+ > | wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1 | Crbellum > Hspt 1 | Cerebellum Adult 8-weeks DNaseI HS Hotspots Rep 1 from > ENCODE/UW | regulation | > | wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1 | Crbellum Pk > 1 | Cerebellum Adult 8-weeks DNaseI HS Peaks Rep 1 from ENCODE/UW > | regulation | > +-------------------------------------------------------+-----------------+------------------------------------------------------------------+------------+ > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
