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 | +-------------------------------------------------------+-----------------+------------------------------------------------------------------+------------+ -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
