deletions | additions       diff --git a/ipynb/Array-systematic-writing.ipynb b/ipynb/Array-systematic-writing.ipynb  index 171ccef..79d59bf 100644  --- a/ipynb/Array-systematic-writing.ipynb  +++ b/ipynb/Array-systematic-writing.ipynb 
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],  "prompt_number": 31  },  {  "cell_type": "heading",  "level": 1,  "metadata": {},  "source": [  "Creating Merged Features 3plus"  ]  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff \\\n",  "> ./analyses/2M_3plusmerge_Hypo.gff \n",  "!head ./analyses/2M_3plusmerge_Hypo.gff \n",  "!wc -l ./analyses/2M_3plusmerge_Hypo.gff \n"  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "scaffold1016\t249436\t249737\r\n",  "scaffold1041\t199217\t199498\r\n",  "scaffold1188\t461425\t461738\r\n",  "scaffold12\t243960\t244376\r\n",  "scaffold1210\t165042\t165474\r\n",  "scaffold1235\t26466\t26785\r\n",  "scaffold1255\t198376\t198802\r\n",  "scaffold1307\t652152\t652606\r\n",  "scaffold1322\t409152\t409472\r\n",  "scaffold1367\t121175\t121233\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 108 ./analyses/2M_3plusmerge_Hypo.gff\r\n"  ]  }  ],  "prompt_number": 36  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff \\\n",  "> ./analyses/2M_3plusmerge_Hyper.gff \n",  "!head ./analyses/2M_3plusmerge_Hyper.gff \n",  "!wc -l ./analyses/2M_3plusmerge_Hyper.gff "  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "scaffold1583\t976276\t976596\r\n",  "scaffold257\t1235165\t1235481\r\n",  "scaffold43954\t139271\t139589\r\n",  "scaffold801\t338541\t338853\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 4 ./analyses/2M_3plusmerge_Hyper.gff\r\n"  ]  }  ],  "prompt_number": 37  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff \\\n",  "> ./analyses/4M_3plusmerge_Hypo.gff \n",  "!head ./analyses/4M_3plusmerge_Hypo.gff \n",  "!wc -l ./analyses/4M_3plusmerge_Hypo.gff "  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "scaffold100\t804406\t804960\r\n",  "scaffold1018\t367127\t367319\r\n",  "scaffold1018\t367618\t367674\r\n",  "scaffold1077\t401205\t401534\r\n",  "scaffold12\t244080\t244376\r\n",  "scaffold1324\t356489\t356781\r\n",  "scaffold1409\t139329\t139505\r\n",  "scaffold1409\t139629\t139680\r\n",  "scaffold142\t656144\t656460\r\n",  "scaffold1484\t346442\t346623\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 48 ./analyses/4M_3plusmerge_Hypo.gff\r\n"  ]  }  ],  "prompt_number": 38  },  {  "cell_type": "code",  "collapsed": false,  "input": [], [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff \\\n",  "> ./analyses/4M_3plusmerge_Hyper.gff \n",  "!head ./analyses/4M_3plusmerge_Hyper.gff \n",  "!wc -l ./analyses/4M_3plusmerge_Hyper.gff "  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "scaffold1241\t28111\t28419\r\n",  "scaffold1447\t305772\t306206\r\n",  "scaffold1805\t257176\t257496\r\n",  "scaffold257\t1235165\t1235481\r\n",  "scaffold40230\t41604\t41898\r\n",  "scaffold41982\t74367\t74671\r\n",  "scaffold63\t426683\t426993\r\n",  "scaffold70\t774778\t775094\r\n",  "scaffold801\t338037\t338345\r\n",  "scaffold801\t339443\t339729\r\n"  ]  },  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 10 ./analyses/4M_3plusmerge_Hyper.gff\r\n"  ]  }  ],  "prompt_number": 39  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff \\\n",  "> ./analyses/2M_3plusmerge_Hypo.gff \n",  "!head ./analyses/2M_3plusmerge_Hypo.gff \n",  "!wc -l ./analyses/2M_3plusmerge_Hypo.gff "  ],  "language": "python",  "metadata": {},  "outputs": []  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!bedtools merge -d 100 -i \\\n",  "./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff \\\n",  "> ./analyses/2M_3plusmerge_Hypo.gff \n",  "!head ./analyses/2M_3plusmerge_Hypo.gff \n",  "!wc -l ./analyses/2M_3plusmerge_Hypo.gff "  ],  "language": "python",  "metadata": {},  "outputs": []  diff --git a/ipynb/analyses/2M_3plusmerge_Hyper.gff b/ipynb/analyses/2M_3plusmerge_Hyper.gff  new file mode 100644  index 0000000..6326e06  --- /dev/null  +++ b/ipynb/analyses/2M_3plusmerge_Hyper.gff 
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scaffold1583 976276 976596  scaffold257 1235165 1235481  scaffold43954 139271 139589  scaffold801 338541 338853  diff --git a/ipynb/analyses/2M_3plusmerge_Hypo.gff b/ipynb/analyses/2M_3plusmerge_Hypo.gff  new file mode 100644  index 0000000..0839eb9  --- /dev/null  +++ b/ipynb/analyses/2M_3plusmerge_Hypo.gff 
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scaffold1016 249436 249737  scaffold1041 199217 199498  scaffold1188 461425 461738  scaffold12 243960 244376  scaffold1210 165042 165474  scaffold1235 26466 26785  scaffold1255 198376 198802  scaffold1307 652152 652606  scaffold1322 409152 409472  scaffold1367 121175 121233  scaffold1367 121440 121625  scaffold1391 190523 190935  scaffold142 237803 238097  scaffold142 656269 656735  scaffold1437 20874 21168  scaffold1497 110217 110525  scaffold150 611097 611397  scaffold1503 67189 67517  scaffold1518 212930 213736  scaffold1532 1408496 1408798  scaffold1625 96879 97439  scaffold1627 214323 214619  scaffold163 482904 483345  scaffold1654 31753 32049  scaffold1656 72301 72470  scaffold1656 72788 72845  scaffold1737 503502 503553  scaffold1737 504057 504108  scaffold1737 504567 504618  scaffold1817 27146 27462  scaffold1835 389934 390487  scaffold189 209552 209991  scaffold1895 133360 133411  scaffold1895 133770 133821  scaffold1895 134200 134258  scaffold1895 134450 134505  scaffold198 550544 550846  scaffold200 34653 34969  scaffold200 35158 35314  scaffold22 1882179 1882231  scaffold22 1882425 1882588  scaffold226 264062 264360  scaffold241 85098 85539  scaffold242 76043 76344  scaffold247 141885 142442  scaffold247 144151 144583  scaffold313 960532 960833  scaffold394 61557 61874  scaffold394 555933 556224  scaffold39778 67963 68284  scaffold39778 68484 68538  scaffold4 76062 76429  scaffold40404 64481 64537  scaffold40404 64745 64917  scaffold40404 65770 65822  scaffold40404 66170 66221  scaffold40404 66370 66421  scaffold406 418360 418767  scaffold406 419005 419060  scaffold406 419330 419384  scaffold406 419660 419718  scaffold40832 34428 34730  scaffold41164 99229 99530  scaffold41900 43748 44054  scaffold42164 95203 95503  scaffold42380 90843 91129  scaffold43 407668 407845  scaffold43 408188 408243  scaffold43036 151198 151505  scaffold43074 200252 200583  scaffold43116 47628 48159  scaffold43258 205910 206238  scaffold44 372931 372983  scaffold44 373276 373703  scaffold44 373851 374293  scaffold44098 96033 96324  scaffold44098 195287 195573  scaffold481 576986 578532  scaffold492 344813 345249  scaffold521 66699 67000  scaffold541 376950 377606  scaffold544 49724 50385  scaffold58 142869 143053  scaffold58 143227 143289  scaffold588 244228 244534  scaffold601 1224731 1225027  scaffold614 224350 224641  scaffold616 239918 240109  scaffold616 240238 240404  scaffold616 240973 241033  scaffold616 282107 282402  scaffold63 419210 419515  scaffold632 252545 252986  scaffold709 412128 412179  scaffold709 412283 412869  scaffold713 340881 341162  scaffold737 107564 107860  scaffold802 110095 110279  scaffold802 110877 110939  scaffold847 550955 551123  scaffold847 551310 551368  scaffold853 46186 46496  scaffold879 121684 121740  scaffold879 121934 122121  scaffold885 474982 475403  scaffold894 42948 43267  scaffold983 16818 17119  scaffold983 17338 18139  diff --git a/ipynb/analyses/4M_3plusmerge_Hyper.gff b/ipynb/analyses/4M_3plusmerge_Hyper.gff  new file mode 100644  index 0000000..5ca24d1  --- /dev/null  +++ b/ipynb/analyses/4M_3plusmerge_Hyper.gff 
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scaffold1241 28111 28419  scaffold1447 305772 306206  scaffold1805 257176 257496  scaffold257 1235165 1235481  scaffold40230 41604 41898  scaffold41982 74367 74671  scaffold63 426683 426993  scaffold70 774778 775094  scaffold801 338037 338345  scaffold801 339443 339729  diff --git a/ipynb/analyses/4M_3plusmerge_Hypo.gff b/ipynb/analyses/4M_3plusmerge_Hypo.gff  new file mode 100644  index 0000000..196af98  --- /dev/null  +++ b/ipynb/analyses/4M_3plusmerge_Hypo.gff 
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scaffold100 804406 804960  scaffold1018 367127 367319  scaffold1018 367618 367674  scaffold1077 401205 401534  scaffold12 244080 244376  scaffold1324 356489 356781  scaffold1409 139329 139505  scaffold1409 139629 139680  scaffold142 656144 656460  scaffold1484 346442 346623  scaffold1484 346732 346793  scaffold1518 212680 212981  scaffold1518 213195 213606  scaffold163 466915 466973  scaffold163 467170 467351  scaffold1759 85559 85855  scaffold1827 304885 305206  scaffold1834 57569 57746  scaffold1834 57946 58006  scaffold1901 351779 352066  scaffold219 171631 171798  scaffold219 171901 171954  scaffold242 75918 76344  scaffold247 141885 142442  scaffold274 459522 460223  scaffold388 212291 212349  scaffold388 213296 213462  scaffold40254 31331 31639  scaffold406 418610 418767  scaffold406 419005 419060  scaffold406 419330 419384  scaffold40856 88091 88283  scaffold40856 88593 88657  scaffold42326 136896 137187  scaffold42788 86761 86949  scaffold42788 87126 87188  scaffold481 577121 578407  scaffold531 87405 87712  scaffold542 250278 250740  scaffold557 401177 401740  scaffold57 375756 376179  scaffold594 259220 259403  scaffold594 259665 259723  scaffold747 349083 349421  scaffold853 46186 46496  scaffold880 495287 495584  scaffold968 118405 118571  scaffold968 118700 118751  diff --git a/ipynb/analyses/6M_3plusmerge_Hyper.gff b/ipynb/analyses/6M_3plusmerge_Hyper.gff  new file mode 100644  index 0000000..8648bad  --- /dev/null  +++ b/ipynb/analyses/6M_3plusmerge_Hyper.gff 
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scaffold1737 485256 485565  scaffold1894 222981 223032  scaffold1894 223601 223653  scaffold1894 224777 224838  scaffold392 326519 326818  scaffold433 204898 205194  scaffold544 44676 44853  scaffold544 45028 45086  scaffold854 353009 353316  diff --git a/ipynb/analyses/6M_3plusmerge_Hypo.gff b/ipynb/analyses/6M_3plusmerge_Hypo.gff  new file mode 100644  index 0000000..48bcee7  --- /dev/null  +++ b/ipynb/analyses/6M_3plusmerge_Hypo.gff 
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scaffold101 610174 610236  scaffold101 610559 610740  scaffold1123 40268 40589  scaffold1204 66531 66832  scaffold1235 34089 34268  scaffold1235 34383 34443  scaffold1249 494779 495082  scaffold1264 68697 69025  scaffold1493 16031 16478  scaffold1719 330025 330079  scaffold1719 330285 330484  scaffold1752 17551 17709  scaffold1752 17916 17975  scaffold193 65914 65965  scaffold193 66130 66185  scaffold193 66310 66371  scaffold203 259584 259908  scaffold247 141885 142442  scaffold247 144031 144583  scaffold308 50213 50645  scaffold335 60010 60067  scaffold335 60531 60693  scaffold348 716142 716446  scaffold372 176523 176578  scaffold372 176916 176971  scaffold372 177146 177197  scaffold392 203896 204208  scaffold392 213620 213932  scaffold394 555813 556110  scaffold40282 64161 64479  scaffold42302 144946 145003  scaffold42302 145180 145356  scaffold43794 261331 261398  scaffold43794 261706 261891  scaffold457 43443 43495  scaffold457 43703 43889  scaffold481 577121 577537  scaffold521 107296 107353  scaffold521 107545 107608  scaffold521 107905 107956  scaffold542 242268 242712  scaffold542 247837 248022  scaffold542 248198 248253  scaffold579 198644 198702  scaffold579 199044 199103  scaffold579 199314 199373  scaffold588 57559 57881  scaffold622 436892 437068  scaffold622 437182 437236  scaffold622 437447 437499  scaffold665 96792 96857  scaffold665 97417 97616  scaffold942 185812 186123