!wc -l /Users/sr320/git-repos/paper-Temp-stress/genome-feature-tracks/*
10028 /Users/sr320/git-repos/paper-Temp-stress/genome-feature-tracks/2014.07.02.2M_sig.bedGraph 10148 /Users/sr320/git-repos/paper-Temp-stress/genome-feature-tracks/2014.07.02.4M_sig.bedGraph 11690 /Users/sr320/git-repos/paper-Temp-stress/genome-feature-tracks/2014.07.02.6M_sig.bedGraph 31866 total
!wc -l /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/*
10028 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.2M_sig.bedGraph 10148 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.4M_sig.bedGraph 11690 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.6M_sig.bedGraph 4 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2M_3plusmerge_Hyper.bed 108 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2M_3plusmerge_Hypo.bed 10 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/4M_3plusmerge_Hyper.bed 48 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/4M_3plusmerge_Hypo.bed 9 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/6M_3plusmerge_Hyper.bed 53 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/6M_3plusmerge_Hypo.bed 32098 total
!bedtools intersect \
-a /Volumes/web/halfshell/2015-05-comgenbro/2M_3plusmerge_Hyper.bed \
-b /Volumes/web/halfshell/2015-05-comgenbro/4M_3plusmerge_Hyper.bed \
/Volumes/web/halfshell/2015-05-comgenbro/6M_3plusmerge_Hyper.bed
scaffold257 1235165 1235481
!bedtools intersect \
-a /Volumes/web/halfshell/2015-05-comgenbro/2M_3plusmerge_Hypo.bed \
-b /Volumes/web/halfshell/2015-05-comgenbro/4M_3plusmerge_Hypo.bed \
/Volumes/web/halfshell/2015-05-comgenbro/6M_3plusmerge_Hypo.bed
scaffold12 244080 244376 scaffold142 656269 656460 scaffold1518 212930 212981 scaffold1518 213195 213606 scaffold242 76043 76344 scaffold247 141885 142442 scaffold247 141885 142442 scaffold247 144151 144583 scaffold394 555933 556110 scaffold406 418610 418767 scaffold406 419005 419060 scaffold406 419330 419384 scaffold481 577121 578407 scaffold481 577121 577537 scaffold853 46186 46496
!cat \
/Volumes/web/halfshell/2015-05-comgenbro/2M_3plusmerge_Hyper.bed \
/Volumes/web/halfshell/2015-05-comgenbro/4M_3plusmerge_Hyper.bed \
/Volumes/web/halfshell/2015-05-comgenbro/6M_3plusmerge_Hyper.bed
scaffold1583 976276 976596 scaffold257 1235165 1235481 scaffold43954 139271 139589 scaffold801 338541 338853 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 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
!cat \
/Volumes/web/halfshell/2015-05-comgenbro/2M_3plusmerge_Hypo.bed \
/Volumes/web/halfshell/2015-05-comgenbro/4M_3plusmerge_Hypo.bed \
/Volumes/web/halfshell/2015-05-comgenbro/6M_3plusmerge_Hypo.bed \
> /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed
!wc -l /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed
209 /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed
!bedtools merge -i /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed
Error: Sorted input specified, but the file /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed has the following out of order record scaffold12 244080 244376
!bedtools sort -i /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcat.bed \
> /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcatsort.bed
!bedtools merge -c 2 -o count \
-i /Users/sr320/git-repos/paper-Temp-stress/ipynb/analyses/mergHYPOcatsort.bed | sort -nrk4
scaffold481 576986 578532 3 scaffold247 141885 142442 3 scaffold1518 212680 213736 3 scaffold853 46186 46496 2 scaffold406 419330 419384 2 scaffold406 419005 419060 2 scaffold406 418360 418767 2 scaffold394 555813 556224 2 scaffold247 144031 144583 2 scaffold242 75918 76344 2 scaffold142 656144 656735 2 scaffold12 243960 244376 2 scaffold983 17338 18139 1 scaffold983 16818 17119 1 scaffold968 118700 118751 1 scaffold968 118405 118571 1 scaffold942 185812 186123 1 scaffold894 42948 43267 1 scaffold885 474982 475403 1 scaffold880 495287 495584 1 scaffold879 121934 122121 1 scaffold879 121684 121740 1 scaffold847 551310 551368 1 scaffold847 550955 551123 1 scaffold802 110877 110939 1 scaffold802 110095 110279 1 scaffold747 349083 349421 1 scaffold737 107564 107860 1 scaffold713 340881 341162 1 scaffold709 412283 412869 1 scaffold709 412128 412179 1 scaffold665 97417 97616 1 scaffold665 96792 96857 1 scaffold632 252545 252986 1 scaffold63 419210 419515 1 scaffold622 437447 437499 1 scaffold622 437182 437236 1 scaffold622 436892 437068 1 scaffold616 282107 282402 1 scaffold616 240973 241033 1 scaffold616 240238 240404 1 scaffold616 239918 240109 1 scaffold614 224350 224641 1 scaffold601 1224731 1225027 1 scaffold594 259665 259723 1 scaffold594 259220 259403 1 scaffold588 57559 57881 1 scaffold588 244228 244534 1 scaffold58 143227 143289 1 scaffold58 142869 143053 1 scaffold579 199314 199373 1 scaffold579 199044 199103 1 scaffold579 198644 198702 1 scaffold57 375756 376179 1 scaffold557 401177 401740 1 scaffold544 49724 50385 1 scaffold542 250278 250740 1 scaffold542 248198 248253 1 scaffold542 247837 248022 1 scaffold542 242268 242712 1 scaffold541 376950 377606 1 scaffold531 87405 87712 1 scaffold521 66699 67000 1 scaffold521 107905 107956 1 scaffold521 107545 107608 1 scaffold521 107296 107353 1 scaffold492 344813 345249 1 scaffold457 43703 43889 1 scaffold457 43443 43495 1 scaffold44098 96033 96324 1 scaffold44098 195287 195573 1 scaffold44 373851 374293 1 scaffold44 373276 373703 1 scaffold44 372931 372983 1 scaffold43794 261706 261891 1 scaffold43794 261331 261398 1 scaffold43258 205910 206238 1 scaffold43116 47628 48159 1 scaffold43074 200252 200583 1 scaffold43036 151198 151505 1 scaffold43 408188 408243 1 scaffold43 407668 407845 1 scaffold42788 87126 87188 1 scaffold42788 86761 86949 1 scaffold42380 90843 91129 1 scaffold42326 136896 137187 1 scaffold42302 145180 145356 1 scaffold42302 144946 145003 1 scaffold42164 95203 95503 1 scaffold41900 43748 44054 1 scaffold41164 99229 99530 1 scaffold40856 88593 88657 1 scaffold40856 88091 88283 1 scaffold40832 34428 34730 1 scaffold406 419660 419718 1 scaffold40404 66370 66421 1 scaffold40404 66170 66221 1 scaffold40404 65770 65822 1 scaffold40404 64745 64917 1 scaffold40404 64481 64537 1 scaffold40282 64161 64479 1 scaffold40254 31331 31639 1 scaffold4 76062 76429 1 scaffold39778 68484 68538 1 scaffold39778 67963 68284 1 scaffold394 61557 61874 1 scaffold392 213620 213932 1 scaffold392 203896 204208 1 scaffold388 213296 213462 1 scaffold388 212291 212349 1 scaffold372 177146 177197 1 scaffold372 176916 176971 1 scaffold372 176523 176578 1 scaffold348 716142 716446 1 scaffold335 60531 60693 1 scaffold335 60010 60067 1 scaffold313 960532 960833 1 scaffold308 50213 50645 1 scaffold274 459522 460223 1 scaffold241 85098 85539 1 scaffold226 264062 264360 1 scaffold22 1882425 1882588 1 scaffold22 1882179 1882231 1 scaffold219 171901 171954 1 scaffold219 171631 171798 1 scaffold203 259584 259908 1 scaffold200 35158 35314 1 scaffold200 34653 34969 1 scaffold198 550544 550846 1 scaffold193 66310 66371 1 scaffold193 66130 66185 1 scaffold193 65914 65965 1 scaffold1901 351779 352066 1 scaffold1895 134450 134505 1 scaffold1895 134200 134258 1 scaffold1895 133770 133821 1 scaffold1895 133360 133411 1 scaffold189 209552 209991 1 scaffold1835 389934 390487 1 scaffold1834 57946 58006 1 scaffold1834 57569 57746 1 scaffold1827 304885 305206 1 scaffold1817 27146 27462 1 scaffold1759 85559 85855 1 scaffold1752 17916 17975 1 scaffold1752 17551 17709 1 scaffold1737 504567 504618 1 scaffold1737 504057 504108 1 scaffold1737 503502 503553 1 scaffold1719 330285 330484 1 scaffold1719 330025 330079 1 scaffold1656 72788 72845 1 scaffold1656 72301 72470 1 scaffold1654 31753 32049 1 scaffold163 482904 483345 1 scaffold163 467170 467351 1 scaffold163 466915 466973 1 scaffold1627 214323 214619 1 scaffold1625 96879 97439 1 scaffold1532 1408496 1408798 1 scaffold1503 67189 67517 1 scaffold150 611097 611397 1 scaffold1497 110217 110525 1 scaffold1493 16031 16478 1 scaffold1484 346732 346793 1 scaffold1484 346442 346623 1 scaffold1437 20874 21168 1 scaffold142 237803 238097 1 scaffold1409 139629 139680 1 scaffold1409 139329 139505 1 scaffold1391 190523 190935 1 scaffold1367 121440 121625 1 scaffold1367 121175 121233 1 scaffold1324 356489 356781 1 scaffold1322 409152 409472 1 scaffold1307 652152 652606 1 scaffold1264 68697 69025 1 scaffold1255 198376 198802 1 scaffold1249 494779 495082 1 scaffold1235 34383 34443 1 scaffold1235 34089 34268 1 scaffold1235 26466 26785 1 scaffold1210 165042 165474 1 scaffold1204 66531 66832 1 scaffold1188 461425 461738 1 scaffold1123 40268 40589 1 scaffold1077 401205 401534 1 scaffold1041 199217 199498 1 scaffold1018 367618 367674 1 scaffold1018 367127 367319 1 scaffold1016 249436 249737 1 scaffold101 610559 610740 1 scaffold101 610174 610236 1 scaffold100 804406 804960 1
!head ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*
==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph <== track type=bedGraph name="2M" description="2M" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 52347 52397 -0.835068225129123 scaffold1 52472 52522 -0.528877734264873 scaffold1 52597 52650 -0.570240181191101 scaffold1 52741 52798 -0.631246435590896 scaffold1 52851 52916 -0.647357503394735 scaffold1 52996 53057 -0.657527480568186 scaffold1 53101 53153 -1.04675017188359 scaffold1 53241 53291 -0.676510028159182 scaffold1 53351 53406 -0.474668524468244 ==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph <== track type=bedGraph name="2M_sig" description="2M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 163391 163444 -1.19635354862016 scaffold1 167390 167448 -1.34858424227208 scaffold1 177036 177092 -1.32513261026528 scaffold1 180263 180313 -1.59644601437398 scaffold1 184151 184202 -1.36802539236446 scaffold1 207852 207911 -1.4489540693628 scaffold1 221645 221697 -1.19168816975966 scaffold100 20261 20311 -1.38705592724581 scaffold100 43707 43766 -1.94554287545546 ==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph <== track type=bedGraph name="4M" description="4M" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 52347 52397 -0.607382638604216 scaffold1 52472 52522 -0.517778984565597 scaffold1 52597 52650 -0.614441888334089 scaffold1 52741 52798 -1.0125546293844 scaffold1 52851 52916 0.170736223516649 scaffold1 52996 53057 -1.05130751246805 scaffold1 53101 53153 -0.793057755493946 scaffold1 53241 53291 -0.661392663616478 scaffold1 53351 53406 -0.643892831771129 ==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph <== track type=bedGraph name="4M_sig" description="4M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 55723 55780 -1.14983078196614 scaffold1 162896 162952 1.31051906307266 scaffold1 165162 165215 -1.24601772855566 scaffold1 171392 171453 -1.22260744814979 scaffold1 174020 174073 1.13065801555915 scaffold1 174287 174343 -1.69319890151177 scaffold1 176273 176334 -1.72785163633438 scaffold1 178210 178267 1.2199265031441 scaffold1 183256 183318 -1.30551922539134 ==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph <== track type=bedGraph name="6M" description="6M" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 52347 52397 -0.445639866598264 scaffold1 52472 52522 -0.0688012470051458 scaffold1 52597 52650 -0.0587539333226483 scaffold1 52741 52798 -0.117394256248887 scaffold1 52851 52916 0.106790241643465 scaffold1 52996 53057 -0.947285682260127 scaffold1 53101 53153 -0.40187966219701 scaffold1 53241 53291 -0.218378761377913 scaffold1 53351 53406 -0.260193541648929 ==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph <== track type=bedGraph name="6M_sig" description="6M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 54599 54654 -1.38187662416007 scaffold1 162129 162191 1.85685479189849 scaffold1 163536 163586 -1.15032035523765 scaffold1 172654 172714 1.33561271440876 scaffold1 174287 174343 -1.62903936976887 scaffold1 178075 178128 1.42323539316231 scaffold1 178685 178740 1.30886296151914 scaffold1 184271 184330 -1.20699853451878 scaffold1 184661 184715 -1.61107459826899
!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*
697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph 10028 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph 697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph 10148 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph 697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph 11690 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph 2125125 total
!fgrep "-" -c ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*
./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph:338556 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph:7224 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph:344889 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph:6560 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph:340387 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph:7645
!head ./data/2014.06.20*
==> ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff <== ==> ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff <==
!wc -l ./data/2014.06.20*
164 ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff 362 ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff 526 total
!head ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff
!bedtools merge -d 100 -i ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff | wc -l
111
!bedtools merge -d 100 -i ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff | wc -l
54
!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.*
12 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff 310 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff 31 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff 127 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff 18 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hyper_3plusAdjactentProbes.gff 108 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hypo_3plusAdjactentProbes.gff 606 total
%%bash
for f in ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.*
do
echo $f
bedtools merge -d 100 -i $f | wc -l
done
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff 4 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff 108 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff 10 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff 48 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hyper_3plusAdjactentProbes.gff 9 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hypo_3plusAdjactentProbes.gff 53
!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff
310 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff \
> ./analyses/2M_3plusmerge_Hypo.gff
!head ./analyses/2M_3plusmerge_Hypo.gff
!wc -l ./analyses/2M_3plusmerge_Hypo.gff
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 108 ./analyses/2M_3plusmerge_Hypo.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff \
> ./analyses/2M_3plusmerge_Hyper.gff
!head ./analyses/2M_3plusmerge_Hyper.gff
!wc -l ./analyses/2M_3plusmerge_Hyper.gff
scaffold1583 976276 976596 scaffold257 1235165 1235481 scaffold43954 139271 139589 scaffold801 338541 338853 4 ./analyses/2M_3plusmerge_Hyper.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff \
> ./analyses/4M_3plusmerge_Hypo.gff
!head ./analyses/4M_3plusmerge_Hypo.gff
!wc -l ./analyses/4M_3plusmerge_Hypo.gff
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 48 ./analyses/4M_3plusmerge_Hypo.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff \
> ./analyses/4M_3plusmerge_Hyper.gff
!head ./analyses/4M_3plusmerge_Hyper.gff
!wc -l ./analyses/4M_3plusmerge_Hyper.gff
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 10 ./analyses/4M_3plusmerge_Hyper.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hypo_3plusAdjactentProbes.gff \
> ./analyses/6M_3plusmerge_Hypo.gff
!head ./analyses/6M_3plusmerge_Hypo.gff
!wc -l ./analyses/6M_3plusmerge_Hypo.gff
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 53 ./analyses/6M_3plusmerge_Hypo.gff
!bedtools merge -d 100 -i \
./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hyper_3plusAdjactentProbes.gff \
> ./analyses/6M_3plusmerge_Hyper.gff
!head ./analyses/6M_3plusmerge_Hyper.gff
!wc -l /analyses/6M_3plusmerge_Hyper.gff
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 9 ./analyses/6M_3plusmerge_Hyper.gff
!ls ./analyses/[2-6]*.gff
./analyses/2M_3plusmerge_Hyper.gff ./analyses/4M_3plusmerge_Hypo.gff ./analyses/2M_3plusmerge_Hypo.gff ./analyses/6M_3plusmerge_Hyper.gff ./analyses/4M_3plusmerge_Hyper.gff ./analyses/6M_3plusmerge_Hypo.gff
!cat ./analyses/[2-6]*.gff | cut -f1 | sort | uniq -c | sort | tail
3 scaffold622 3 scaffold801 4 scaffold1737 4 scaffold1895 4 scaffold521 4 scaffold542 4 scaffold616 5 scaffold247 5 scaffold40404 7 scaffold406
!head /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.6M_sig.bedGraph
track type=bedGraph name="6M_sig" description="6M_sig" visibility=full color=100,100,0 altColor=0,100,200 priority=20 scaffold1 54599 54654 -1.38187662416007 scaffold1 162129 162191 1.85685479189849 scaffold1 163536 163586 -1.15032035523765 scaffold1 172654 172714 1.33561271440876 scaffold1 174287 174343 -1.62903936976887 scaffold1 178075 178128 1.42323539316231 scaffold1 178685 178740 1.30886296151914 scaffold1 184271 184330 -1.20699853451878 scaffold1 184661 184715 -1.61107459826899
!wc /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.6M_sig.bedGraph
11690 46764 509521 /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.6M_sig.bedGraph
!bedtools merge -d 500 -i \
/Users/sr320/git-repos/paper-Temp-stress/ipynb/data/canonical/2014.07.02.6M_sig.bedGraph \
| wc -l
10287