this is for holding javascript data
Steven Roberts Merge pull request #14 from sr320/master
edited results-array.md
about 9 years ago
Commit id: 8499b94ede8ce6dc6e2c927b41db6b4427b1fac4
deletions | additions
diff --git a/ipynb/.ipynb_checkpoints/Array-systematic-writing-checkpoint.ipynb b/ipynb/.ipynb_checkpoints/Array-systematic-writing-checkpoint.ipynb
index e8cb62e..7cf8795 100644
--- a/ipynb/.ipynb_checkpoints/Array-systematic-writing-checkpoint.ipynb
+++ b/ipynb/.ipynb_checkpoints/Array-systematic-writing-checkpoint.ipynb
...
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"input": [
"!head ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*"
],
"language": "python",
"metadata": {},
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{
"output_type": "stream",
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"text": [
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph <==\r\n",
"track type=bedGraph name=\"2M\" description=\"2M\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t52347\t52397\t-0.835068225129123\r\n",
"scaffold1\t52472\t52522\t-0.528877734264873\r\n",
"scaffold1\t52597\t52650\t-0.570240181191101\r\n",
"scaffold1\t52741\t52798\t-0.631246435590896\r\n",
"scaffold1\t52851\t52916\t-0.647357503394735\r\n",
"scaffold1\t52996\t53057\t-0.657527480568186\r\n",
"scaffold1\t53101\t53153\t-1.04675017188359\r\n",
"scaffold1\t53241\t53291\t-0.676510028159182\r\n",
"scaffold1\t53351\t53406\t-0.474668524468244\r\n",
"\r\n",
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph <==\r\n",
"track type=bedGraph name=\"2M_sig\" description=\"2M_sig\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t163391\t163444\t-1.19635354862016\r\n",
"scaffold1\t167390\t167448\t-1.34858424227208\r\n",
"scaffold1\t177036\t177092\t-1.32513261026528\r\n",
"scaffold1\t180263\t180313\t-1.59644601437398\r\n",
"scaffold1\t184151\t184202\t-1.36802539236446\r\n",
"scaffold1\t207852\t207911\t-1.4489540693628\r\n",
"scaffold1\t221645\t221697\t-1.19168816975966\r\n",
"scaffold100\t20261\t20311\t-1.38705592724581\r\n",
"scaffold100\t43707\t43766\t-1.94554287545546\r\n",
"\r\n",
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph <==\r\n",
"track type=bedGraph name=\"4M\" description=\"4M\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t52347\t52397\t-0.607382638604216\r\n",
"scaffold1\t52472\t52522\t-0.517778984565597\r\n",
"scaffold1\t52597\t52650\t-0.614441888334089\r\n",
"scaffold1\t52741\t52798\t-1.0125546293844\r\n",
"scaffold1\t52851\t52916\t0.170736223516649\r\n",
"scaffold1\t52996\t53057\t-1.05130751246805\r\n",
"scaffold1\t53101\t53153\t-0.793057755493946\r\n",
"scaffold1\t53241\t53291\t-0.661392663616478\r\n",
"scaffold1\t53351\t53406\t-0.643892831771129\r\n",
"\r\n",
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph <==\r\n",
"track type=bedGraph name=\"4M_sig\" description=\"4M_sig\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t55723\t55780\t-1.14983078196614\r\n",
"scaffold1\t162896\t162952\t1.31051906307266\r\n",
"scaffold1\t165162\t165215\t-1.24601772855566\r\n",
"scaffold1\t171392\t171453\t-1.22260744814979\r\n",
"scaffold1\t174020\t174073\t1.13065801555915\r\n",
"scaffold1\t174287\t174343\t-1.69319890151177\r\n",
"scaffold1\t176273\t176334\t-1.72785163633438\r\n",
"scaffold1\t178210\t178267\t1.2199265031441\r\n",
"scaffold1\t183256\t183318\t-1.30551922539134\r\n",
"\r\n",
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph <==\r\n",
"track type=bedGraph name=\"6M\" description=\"6M\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t52347\t52397\t-0.445639866598264\r\n",
"scaffold1\t52472\t52522\t-0.0688012470051458\r\n",
"scaffold1\t52597\t52650\t-0.0587539333226483\r\n",
"scaffold1\t52741\t52798\t-0.117394256248887\r\n",
"scaffold1\t52851\t52916\t0.106790241643465\r\n",
"scaffold1\t52996\t53057\t-0.947285682260127\r\n",
"scaffold1\t53101\t53153\t-0.40187966219701\r\n",
"scaffold1\t53241\t53291\t-0.218378761377913\r\n",
"scaffold1\t53351\t53406\t-0.260193541648929\r\n",
"\r\n",
"==> ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph <==\r\n",
"track type=bedGraph name=\"6M_sig\" description=\"6M_sig\" visibility=full color=100,100,0 altColor=0,100,200 priority=20\r\n",
"scaffold1\t54599\t54654\t-1.38187662416007\r\n",
"scaffold1\t162129\t162191\t1.85685479189849\r\n",
"scaffold1\t163536\t163586\t-1.15032035523765\r\n",
"scaffold1\t172654\t172714\t1.33561271440876\r\n",
"scaffold1\t174287\t174343\t-1.62903936976887\r\n",
"scaffold1\t178075\t178128\t1.42323539316231\r\n",
"scaffold1\t178685\t178740\t1.30886296151914\r\n",
"scaffold1\t184271\t184330\t-1.20699853451878\r\n",
"scaffold1\t184661\t184715\t-1.61107459826899\r\n"
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"input": [
"!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*"
],
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"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph\r\n",
" 10028 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph\r\n",
" 10148 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 697753 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph\r\n",
" 11690 ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph\r\n",
" 2125125 total\r\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!fgrep \"-\" -c ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/*"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M.bedGraph:338556\r\n",
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph:7224\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M.bedGraph:344889\r\n",
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph:6560\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M.bedGraph:340387\r\n",
"./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph:7645\r\n"
]
}
],
"prompt_number": 3
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{
"cell_type": "code",
"collapsed": false,
"input": [
"\n",
"!head ./data/2014.06.20*"
],
"language": "python",
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{
"output_type": "stream",
"stream": "stdout",
"text": [
"==> ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff <==\r\n",
"scaffold100\tOysterV9\tprobes\t636974\t637034\t1\t.\t.\tscaffold100:+:636974\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t637084\t637143\t1\t.\t.\tscaffold100:+:637084\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t637209\t637276\t1\t.\t.\tscaffold100:+:637209\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303196\t303251\t1\t.\t.\tscaffold102:+:303196\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303336\t303394\t1\t.\t.\tscaffold102:+:303336\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303521\t303576\t1\t.\t.\tscaffold102:+:303521\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634021\t634085\t1\t.\t.\tscaffold1032:+:634021\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634156\t634218\t1\t.\t.\tscaffold1032:+:634156\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634281\t634333\t1\t.\t.\tscaffold1032:+:634281\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t700173\t700230\t1\t.\t.\tscaffold1032:+:700173\r",
"\r\n",
"\r\n",
"==> ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff <==\r\n",
"scaffold100\tOysterV9\tprobes\t804272\t804322\t1\t.\t.\tscaffold100:+:804272\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804407\t804457\t1\t.\t.\tscaffold100:+:804407\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804532\t804582\t1\t.\t.\tscaffold100:+:804532\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804652\t804703\t1\t.\t.\tscaffold100:+:804652\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804787\t804844\t1\t.\t.\tscaffold100:+:804787\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804897\t804960\t1\t.\t.\tscaffold100:+:804897\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805157\t805213\t1\t.\t.\tscaffold100:+:805157\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805287\t805337\t1\t.\t.\tscaffold100:+:805287\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805402\t805452\t1\t.\t.\tscaffold100:+:805402\r",
"\r\n",
"scaffold1016\tOysterV9\tprobes\t202657\t202722\t1\t.\t.\tscaffold1016:+:202657\r",
"\r\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l ./data/2014.06.20*"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 164 ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff\r\n",
" 362 ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff\r\n",
" 526 total\r\n"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"scaffold100\tOysterV9\tprobes\t804272\t804322\t1\t.\t.\tscaffold100:+:804272\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804407\t804457\t1\t.\t.\tscaffold100:+:804407\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804532\t804582\t1\t.\t.\tscaffold100:+:804532\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804652\t804703\t1\t.\t.\tscaffold100:+:804652\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804787\t804844\t1\t.\t.\tscaffold100:+:804787\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804897\t804960\t1\t.\t.\tscaffold100:+:804897\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805157\t805213\t1\t.\t.\tscaffold100:+:805157\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805287\t805337\t1\t.\t.\tscaffold100:+:805287\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805402\t805452\t1\t.\t.\tscaffold100:+:805402\r",
"\r\n",
"scaffold1016\tOysterV9\tprobes\t202657\t202722\t1\t.\t.\tscaffold1016:+:202657\r",
"\r\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Merging Adjacent "
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!bedtools merge -d 100 -i ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff | wc -l\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 111\r\n"
]
}
],
"prompt_number": 20
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!bedtools merge -d 100 -i ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff | wc -l\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 54\r\n"
]
}
],
"prompt_number": 21
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 12 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff\r\n"
]
}
],
"prompt_number": 24
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 310 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff\r\n"
]
}
],
"prompt_number": 25
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
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diff --git a/ipynb/Array-systematic-writing.ipynb b/ipynb/Array-systematic-writing.ipynb
index 23f9768..171ccef 100644
--- a/ipynb/Array-systematic-writing.ipynb
+++ b/ipynb/Array-systematic-writing.ipynb
...
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"input": [
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"!head ./data/2014.06.20*"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"==> ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff <==\r\n",
"scaffold100\tOysterV9\tprobes\t636974\t637034\t1\t.\t.\tscaffold100:+:636974\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t637084\t637143\t1\t.\t.\tscaffold100:+:637084\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t637209\t637276\t1\t.\t.\tscaffold100:+:637209\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303196\t303251\t1\t.\t.\tscaffold102:+:303196\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303336\t303394\t1\t.\t.\tscaffold102:+:303336\r",
"\r\n",
"scaffold102\tOysterV9\tprobes\t303521\t303576\t1\t.\t.\tscaffold102:+:303521\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634021\t634085\t1\t.\t.\tscaffold1032:+:634021\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634156\t634218\t1\t.\t.\tscaffold1032:+:634156\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t634281\t634333\t1\t.\t.\tscaffold1032:+:634281\r",
"\r\n",
"scaffold1032\tOysterV9\tprobes\t700173\t700230\t1\t.\t.\tscaffold1032:+:700173\r",
"\r\n",
"\r\n",
"==> ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff <==\r\n",
"scaffold100\tOysterV9\tprobes\t804272\t804322\t1\t.\t.\tscaffold100:+:804272\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804407\t804457\t1\t.\t.\tscaffold100:+:804407\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804532\t804582\t1\t.\t.\tscaffold100:+:804532\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804652\t804703\t1\t.\t.\tscaffold100:+:804652\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804787\t804844\t1\t.\t.\tscaffold100:+:804787\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804897\t804960\t1\t.\t.\tscaffold100:+:804897\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805157\t805213\t1\t.\t.\tscaffold100:+:805157\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805287\t805337\t1\t.\t.\tscaffold100:+:805287\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805402\t805452\t1\t.\t.\tscaffold100:+:805402\r",
"\r\n",
"scaffold1016\tOysterV9\tprobes\t202657\t202722\t1\t.\t.\tscaffold1016:+:202657\r",
"\r\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l ./data/2014.06.20*"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 164 ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff\r\n",
" 362 ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff\r\n",
" 526 total\r\n"
]
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"scaffold100\tOysterV9\tprobes\t804272\t804322\t1\t.\t.\tscaffold100:+:804272\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804407\t804457\t1\t.\t.\tscaffold100:+:804407\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804532\t804582\t1\t.\t.\tscaffold100:+:804532\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804652\t804703\t1\t.\t.\tscaffold100:+:804652\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804787\t804844\t1\t.\t.\tscaffold100:+:804787\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t804897\t804960\t1\t.\t.\tscaffold100:+:804897\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805157\t805213\t1\t.\t.\tscaffold100:+:805157\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805287\t805337\t1\t.\t.\tscaffold100:+:805287\r",
"\r\n",
"scaffold100\tOysterV9\tprobes\t805402\t805452\t1\t.\t.\tscaffold100:+:805402\r",
"\r\n",
"scaffold1016\tOysterV9\tprobes\t202657\t202722\t1\t.\t.\tscaffold1016:+:202657\r",
"\r\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Merging Adjacent "
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!bedtools merge -d 100 -i ./data/2014.06.20.lt1.8_gt3adjactentProbes.gff | wc -l\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 111\r\n"
]
}
],
"prompt_number": 20
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!bedtools merge -d 100 -i ./data/2014.06.20.gt1.8_gt3adjactentProbes.gff | wc -l\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 54\r\n"
]
}
],
"prompt_number": 21
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc -l ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.*\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 12 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff\r\n",
" 310 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff\r\n",
" 31 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff\r\n",
" 127 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff\r\n",
" 18 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hyper_3plusAdjactentProbes.gff\r\n",
" 108 ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hypo_3plusAdjactentProbes.gff\r\n",
" 606 total\r\n"
]
}
],
"prompt_number": 26
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"%%bash\n",
"for f in ./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.*\n",
"do\n",
"echo $f\n",
"bedtools merge -d 100 -i $f | wc -l\n",
"done\n",
"\n",
"\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hyper_3plusAdjactentProbes.gff\n",
" 4\n",
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.2M_Hypo_3plusAdjactentProbes.gff\n",
" 108\n",
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hyper_3plusAdjactentProbes.gff\n",
" 10\n",
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.4M_Hypo_3plusAdjactentProbes.gff\n",
" 48\n",
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hyper_3plusAdjactentProbes.gff\n",
" 9\n",
"./data/2014.07.02.colson/genomeBrowserTracks/threeOrMoreAdjacentSigProbes/2014.07.02.6M_Hypo_3plusAdjactentProbes.gff\n",
" 53\n"
]
}
],
"prompt_number": 31
},
{
"cell_type": "code",
"collapsed": false,
diff --git a/results-array.md b/results-array.md
index 708b1fb..2c7e365 100644
--- a/results-array.md
+++ b/results-array.md
...
#results-array
In direct comparison of methylation for an individual oyster prior to and following
heat shock approximately 10k differentially methylated features were identified. For all oysters a majority of the features were hypomethylated. Specifically, for oysters #2, #4, and #6 the number of hypomethylated features was 7224, 6560, and 7645, respectively. When only features were considered where at least 3 adjacent probes were also differentially methylated the number of features (merged) for oysters #2, #4, and #6 was 112, 58, and 62, respectively. A majority of these features were hypomethylated (108, 48, and 53, respectively)
Oyster | Hypo-probes | Hyper-probes | Hypo-3plus-merged | Hypo-3plus-merged
--- | --- | --- | --- | ---
2 | 7224 | 2803 | 108 | 4
4 | 6560 | 3587 | 48 | 10
6 | 7645 | 4044 | 53 | 9
In order to examine regions that were differentially methylated across all three oysters features were identified where there were at least 3 adjacent probes with signficantly differentially methylated. A total of 111 features were identified as hypomethylated and 54 features as hypermethylated when differentially methylated probe with 100bp were merged.
Does this go
