Hi I have a problem running the hgGcPercent | wigEncode program(s). I noticed that the winsize is muliplied with 1024. I try to calculate the GC content for a 150 bp window
line executed: hgGcPercent -wigOut -file=stdout -noDots -noLoad -win=150 yeast ./yeast.2bit | /home/hinri/bin/x86_64/wigEncode stdin yeast_gc150bp.wig yeast_gc150bp.wib yields the following wig file. chrI 0 153600 chrI.0 150 1024 0 gc150bp_mb05.wib 19.3 40.7 1024 40252.8 1.62621e+06 chrI 153600 230100 chrI.1 150 510 1024 gc150bp_mb05.wib 22.7 42 510 19980 805250 chrII 0 153600 chrII.2 150 1024 1534 gc150bp_mb05.wib 17.3 43.4 1024 39434.4 1.55141e+06 chrII 153600 307200 chrII.3 150 1024 2558 gc150bp_mb05.wib 14 46 1024 39245.2 1.53911e+06 chrII 307200 460800 chrII.4 150 1024 3582 gc150bp_mb05.wib 18.7 38 1024 38888.2 1.50537e+06 chrII 460800 614400 chrII.5 150 1024 4606 gc150bp_mb05.wib 20.7 38.6 1024 38905.1 1.5059e+06 chrII 614400 768000 chrII.6 150 1024 5630 gc150bp_mb05.wib 21.3 34.7 1024 39851.1 1.5833e+06 chrII 768000 813150 chrII.7 150 301 6654 gc150bp_mb05.wib 20.7 30.6 301 11536.4 450459 chrIII 0 153600 chrIII.8 150 1024 6955 gc150bp_mb05.wib 16.7 45.3 1024 39402.2 1.55913e+06 chrIII 153600 307200 chrIII.9 150 1024 7979 gc150bp_mb05.wib 16.7 42 1024 39508.4 1.56913e+06 chrIII 307200 316500 chrIII.10 150 62 9003 gc150bp_mb05.wib 28 24 62 2376.1 93083.1 chrIV 0 153600 chrIV.11 150 1024 9065 gc150bp_mb05.wib 14.7 47.3 1024 39596.7 1.56501e+06 chrIV 153600 307200 chrIV.12 150 1024 10089 gc150bp_mb05.wib 15.3 38.7 1024 39205.3 1.52896e+06 chrIV 307200 460800 chrIV.13 150 1024 11113 gc150bp_mb05.wib 18 44.7 1024 38711.7 1.49712e+06 chrIV 460800 614400 chrIV.14 150 1024 12137 gc150bp_mb05.wib 16 40 1024 38396 1.47019e+06 chrIV 614400 768000 chrIV.15 150 1024 13161 gc150bp_mb05.wib 19.3 37.4 1024 38637.4 1.48365e+06 chrIV 768000 921600 chrIV.16 150 1024 14185 gc150bp_mb05.wib 20.7 41.3 1024 38568.3 1.48434e+06 chrIV 921600 1075200 chrIV.17 150 1024 15209 gc150bp_mb05.wib 18.7 39.3 1024 38457.9 1.47212e+06 chrIV 1075200 1228800 chrIV.18 150 1024 16233 gc150bp_mb05.wib 20.7 33.3 1024 38075.1 1.44224e+06 chrIV 1228800 1382400 chrIV.19 150 1024 17257 gc150bp_mb05.wib 16 52.7 1024 39225.6 1.53547e+06 chrIV 1382400 1531800 chrIV.20 150 996 18281 gc150bp_mb05.wib 20.7 37.3 996 38234.1 1.50435e+06 chrIX 0 153600 chrIX.21 150 1024 19277 gc150bp_mb05.wib 14.7 46 1024 39897.3 1.59579e+06 chrIX 153600 307200 chrIX.22 150 1024 20301 gc150bp_mb05.wib 18 38 1024 39420.1 1.55406e+06 chrIX 307200 439800 chrIX.23 150 884 21325 gc150bp_mb05.wib 16 40.7 884 34730.7 1.39259e+06 chrM 0 85650 chrM.24 150 571 22209 gc150bp_mb05.wib 0.7 50.6 571 9766.4 225288 chrV 0 153600 chrV.25 150 1024 22780 gc150bp_mb05.wib 15.3 45.4 1024 39367.9 1.55423e+06 chrV 153600 307200 chrV.26 150 1024 23804 gc150bp_mb05.wib 18 43.3 1024 39515.7 1.55911e+06 chrV 307200 460800 chrV.27 150 1024 24828 gc150bp_mb05.wib 14.7 46 1024 39029 1.52323e+06 chrV 460800 576750 chrV.28 150 773 25852 gc150bp_mb05.wib 19.3 40 773 30145.7 1.20341e+06 chrVI 0 153600 chrVI.29 150 1024 26625 gc150bp_mb05.wib 15.3 42.7 1024 39588.5 1.56581e+06 chrVI 153600 270000 chrVI.30 150 776 27649 gc150bp_mb05.wib 20 42.7 776 30119.6 1.1982e+06 chrVII 0 153600 chrVII.31 150 1024 28425 gc150bp_mb05.wib 18 34.7 1024 38738.2 1.4982e+06 chrVII 153600 307200 chrVII.32 150 1024 29449 gc150bp_mb05.wib 22 44 1024 38957.5 1.51432e+06 chrVII 307200 460800 chrVII.33 150 1024 30473 gc150bp_mb05.wib 15.3 42.7 1024 39205.6 1.53546e+06 chrVII 460800 614400 chrVII.34 150 1024 31497 gc150bp_mb05.wib 12.7 46 1024 38866.1 1.50845e+06 chrVII 614400 768000 chrVII.35 150 1024 32521 gc150bp_mb05.wib 20 41.3 1024 38750 1.49858e+06 chrVII 768000 921600 chrVII.36 150 1024 33545 gc150bp_mb05.wib 22 36.7 1024 38946.2 1.51459e+06 chrVII 921600 1075200 chrVII.37 150 1024 34569 gc150bp_mb05.wib 17.3 40 1024 39063.3 1.51911e+06 chrVII 1075200 1090800 chrVII.38 150 104 35593 gc150bp_mb05.wib 26 26.7 104 4250.1 177171 chrVIII 0 153600 chrVIII.39 150 1024 35697 gc150bp_mb05.wib 19.3 38.7 1024 39268.7 1.54304e+06 chrVIII 153600 307200 chrVIII.40 150 1024 36721 gc150bp_mb05.wib 20 38.7 1024 39440.5 1.55467e+06 chrVIII 307200 460800 chrVIII.41 150 1024 37745 gc150bp_mb05.wib 14.7 38 1024 39197.2 1.52984e+06 chrVIII 460800 562500 chrVIII.42 150 678 38769 gc150bp_mb05.wib 20.7 38 678 26420.2 1.05476e+06 chrX 0 153600 chrX.43 150 1024 39447 gc150bp_mb05.wib 13.3 41.4 1024 39378.3 1.54728e+06 chrX 153600 307200 chrX.44 150 1024 40471 gc150bp_mb05.wib 22.7 35.3 1024 39068.4 1.52089e+06 chrX 307200 460800 chrX.45 150 1024 41495 gc150bp_mb05.wib 13.3 47.4 1024 39072.1 1.52568e+06 chrX 460800 614400 chrX.46 150 1024 42519 gc150bp_mb05.wib 21.3 35.4 1024 39341.5 1.54235e+06 chrX 614400 745650 chrX.47 150 875 43543 gc150bp_mb05.wib 20.7 44.6 875 33881.3 1.33957e+06 chrXI 0 153600 chrXI.48 150 1024 44418 gc150bp_mb05.wib 7.3 54.7 1024 39110 1.52884e+06 chrXI 153600 307200 chrXI.49 150 1024 45442 gc150bp_mb05.wib 20.7 46.6 1024 38949.9 1.51259e+06 chrXI 307200 460800 chrXI.50 150 1024 46466 gc150bp_mb05.wib 14.7 44.6 1024 38784.5 1.50226e+06 chrXI 460800 614400 chrXI.51 150 1024 47490 gc150bp_mb05.wib 20.7 41.3 1024 39349.7 1.54718e+06 chrXI 614400 666450 chrXI.52 150 347 48514 gc150bp_mb05.wib 23.3 36.7 347 12957 494568 chrXII 0 153600 chrXII.53 150 1024 48861 gc150bp_mb05.wib 16 43.3 1024 39627.2 1.56929e+06 chrXII 153600 307200 chrXII.54 150 1024 49885 gc150bp_mb05.wib 19.3 40.7 1024 38955.6 1.51248e+06 chrXII 307200 460800 chrXII.55 150 1024 50909 gc150bp_mb05.wib 19.3 44 1024 39933.6 1.59268e+06 chrXII 460800 614400 chrXII.56 150 1024 51933 gc150bp_mb05.wib 20 43.3 1024 40405.9 1.6326e+06 chrXII 614400 768000 chrXII.57 150 1024 52957 gc150bp_mb05.wib 20 43.3 1024 38373.4 1.46896e+06 chrXII 768000 921600 chrXII.58 150 1024 53981 gc150bp_mb05.wib 22 36 1024 39440.5 1.55245e+06 chrXII 921600 1075200 chrXII.59 150 1024 55005 gc150bp_mb05.wib 21.3 40 1024 38928.5 1.51374e+06 chrXII 1075200 1078050 chrXII.60 150 19 56029 gc150bp_mb05.wib 32.7 20.6 19 865.4 39917.5 chrXIII 0 153600 chrXIII.61 150 1024 56048 gc150bp_mb05.wib 16.7 51.3 1024 39566.2 1.56316e+06 chrXIII 153600 307200 chrXIII.62 150 1024 57072 gc150bp_mb05.wib 12 50 1024 39052.8 1.52604e+06 chrXIII 307200 460800 chrXIII.63 150 1024 58096 gc150bp_mb05.wib 15.3 44.7 1024 39008.8 1.51724e+06 chrXIII 460800 614400 chrXIII.64 150 1024 59120 gc150bp_mb05.wib 19.3 38 1024 38705.4 1.4923e+06 chrXIII 614400 768000 chrXIII.65 150 1024 60144 gc150bp_mb05.wib 22.7 32 1024 38861 1.5027e+06 chrXIII 768000 921600 chrXIII.66 150 1024 61168 gc150bp_mb05.wib 20.7 38.6 1024 39498.9 1.55563e+06 chrXIII 921600 924300 chrXIII.67 150 18 62192 gc150bp_mb05.wib 25.3 27.4 18 698.7 28014 chrXIV 0 153600 chrXIV.68 150 1024 62210 gc150bp_mb05.wib 18.7 40 1024 40231 1.61325e+06 chrXIV 153600 307200 chrXIV.69 150 1024 63234 gc150bp_mb05.wib 19.3 43.4 1024 39167 1.53067e+06 chrXIV 307200 460800 chrXIV.70 150 1024 64258 gc150bp_mb05.wib 21.3 38 1024 39308.7 1.53877e+06 chrXIV 460800 614400 chrXIV.71 150 1024 65282 gc150bp_mb05.wib 20 38.7 1024 39263.6 1.53755e+06 chrXIV 614400 768000 chrXIV.72 150 1024 66306 gc150bp_mb05.wib 21.3 38 1024 39792.5 1.57987e+06 chrXIV 768000 784200 chrXIV.73 150 108 67330 gc150bp_mb05.wib 25.3 36.7 108 4210.9 168169 chrXV 0 153600 chrXV.74 150 1024 67438 gc150bp_mb05.wib 18.7 44.6 1024 38879.5 1.51022e+06 chrXV 153600 307200 chrXV.75 150 1024 68462 gc150bp_mb05.wib 19.3 43.4 1024 39548 1.56154e+06 chrXV 307200 460800 chrXV.76 150 1024 69486 gc150bp_mb05.wib 15.3 37.4 1024 38845.4 1.50399e+06 chrXV 460800 614400 chrXV.77 150 1024 70510 gc150bp_mb05.wib 19.3 42 1024 39161.8 1.53013e+06 chrXV 614400 768000 chrXV.78 150 1024 71534 gc150bp_mb05.wib 18 42.7 1024 38665.9 1.49296e+06 chrXV 768000 921600 chrXV.79 150 1024 72558 gc150bp_mb05.wib 22 35.3 1024 38832.2 1.5013e+06 chrXV 921600 1075200 chrXV.80 150 1024 73582 gc150bp_mb05.wib 20.7 42 1024 39292.3 1.54201e+06 chrXV 1075200 1091250 chrXV.81 150 107 74606 gc150bp_mb05.wib 24.7 29.3 107 4390.9 184861 chrXVI 0 153600 chrXVI.82 150 1024 74713 gc150bp_mb05.wib 19.3 38.7 1024 39822.6 1.58172e+06 chrXVI 153600 307200 chrXVI.83 150 1024 75737 gc150bp_mb05.wib 21.3 38.7 1024 38476.5 1.47327e+06 chrXVI 307200 460800 chrXVI.84 150 1024 76761 gc150bp_mb05.wib 18 40.7 1024 38665.2 1.49246e+06 chrXVI 460800 614400 chrXVI.85 150 1024 77785 gc150bp_mb05.wib 12 48 1024 39050.3 1.52073e+06 chrXVI 614400 768000 chrXVI.86 150 1024 78809 gc150bp_mb05.wib 17.3 44 1024 38946.9 1.51218e+06 chrXVI 768000 921600 chrXVI.87 150 1024 79833 gc150bp_mb05.wib 10 52 1024 38913 1.51411e+06 chrXVI 921600 948000 chrXVI.88 150 176 80857 gc150bp_mb05.wib 24 31.3 176 6692.1 261414 The interval is 153600 (which is 1024x150) instead of the requested 150 bp. Has somethings changed since i used it before without any problems. Regards Kees-Jan _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
