{
"metadata": {
"name": "",
"signature": "sha256:daca025075ea76c53f1aebabcab7c2d58040f14d10a54d74a6a7da0a763edd5b"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#Larval Transcriptome of OsHV exposed oysters\n",
"A re-examination of Cgigas larval transcriptome using genome.\n",
"\n",
"\n",
"\n",
"---\n",
"Solid Files -- http://eagle.fish.washington.edu/whale/index.php?dir=GE%2Freads%2F \n",
"\n",
"Importing into CLCv6\n",
"\n",
"###Quality trim \n",
"`\n",
" Ambiguous trim = Yes\n",
" Ambiguous limit = 2\n",
" Quality trim = Yes\n",
" Quality limit = 0.05\n",
" Create report = Yes\n",
" Save discarded sequences = No\n",
" Remove 5' terminal nucleotides = No\n",
" Minimum number of nucleotides in reads = 20\n",
" Discard short reads = Yes\n",
" Remove 3' terminal nucleotides = No\n",
" Discard long reads = No\n",
" Save broken pairs = No\n",
"`\n",
"\n",
"\n",
"\n",
"###QC Report\n",
"\n",
"\n",
"\n",
"###Mapping to Transcriptome\n",
"\n",
"RNA-seq to genes\n",
"\n",
"Parameters \n",
"\n",
"`\n",
" Use strand specific assembly = No\n",
" Create report = Yes\n",
" References = oyster_v9_gene\n",
" Count paired reads as two = No\n",
" Use colorspace encoding = Yes\n",
" Minimum number of reads = 10\n",
" Additional upstream bases = 0\n",
" Minimum read count fusion gene table = 5\n",
" Minimum length of putative exons = 25\n",
" Minimum exon coverage fraction = 0.2\n",
" Minimum length fraction (long reads) = 0.9\n",
" Use annotations for gene and transcript identification = No\n",
" Create fusion gene table = No\n",
" Expression value = TOTAL_GENE_COUNT\n",
" Minimum similarity fraction = 0.8\n",
" Expression level = Genes\n",
" Create list of unmapped reads = No\n",
" Unspecific match limit = 5\n",
" Exon discovery = No\n",
" Organism type = PROKARYOTE\n",
" Additional downstream bases = 0\n",
" Maximum paired distance = 250\n",
" Minimum paired distance = 180\n",
" Strand = Forward\n",
" Maximum number of mismatches allowed (applies to short reads) = 2\n",
" Expression value = Number of reads mapped to the gene\n",
"` \n",
"\n",
"\n",
"\n",
"\n",
"\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#tab delim RNA-Seq file\n",
"!head /Volumes/web/cnidarian/solid0078_20091105_RobertsLab_GE_F3\\ trimmed\\ RNA-Seq.txt"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\"Feature ID\"\t\"Expression values\"\t\"Gene length\"\t\"Unique gene reads\"\t\"Total gene reads\"\t\"RPKM\"\r\n",
"CGI_10000780\t2\t1350\t2\t2\t0.272\r\n",
"CGI_10000456\t28\t438\t18\t28\t11.735\r\n",
"CGI_10000457\t5\t603\t4\t5\t1.522\r\n",
"CGI_10000774\t1\t375\t1\t1\t0.49\r\n",
"CGI_10000917\t2\t426\t2\t2\t0.862\r\n",
"CGI_10000861\t7\t2004\t7\t7\t0.641\r\n",
"CGI_10000994\t96\t1635\t74\t96\t10.779\r\n",
"CGI_10000643\t0\t552\t0\t0\t0\r\n",
"CGI_10000763\t4\t249\t4\t4\t2.949\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#SAM output\n",
"!head /Volumes/web/cnidarian/solid0078_20091105_RobertsLab_GE_F3_tr_RNA-Seq.sam"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"@HD\tVN:1.0\tSO:unsorted\r\n",
"@SQ\tSN:CGI_10000780\tLN:1350\r\n",
"@SQ\tSN:CGI_10000456\tLN:438\r\n",
"@SQ\tSN:CGI_10000457\tLN:603\r\n",
"@SQ\tSN:CGI_10000774\tLN:375\r\n",
"@SQ\tSN:CGI_10000917\tLN:426\r\n",
"@SQ\tSN:CGI_10000861\tLN:2004\r\n",
"@SQ\tSN:CGI_10000994\tLN:1635\r\n",
"@SQ\tSN:CGI_10000643\tLN:552\r\n",
"@SQ\tSN:CGI_10000763\tLN:249\r\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#SAM output\n",
"!tail /Volumes/web/cnidarian/solid0078_20091105_RobertsLab_GE_F3_tr_RNA-Seq.sam"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"read_5447380\t0\tCGI_10003117\t263\t60\t50M\t*\t0\t0\tCCTCGCATTGGAAAACCCCAGTGTTTGGGTGGGTGTCACAAGAGGAAGAA\t@A@?B=AA;@BB@:@:;<=2;>6:?98>:77/7\tNH:i:1\tCS:Z:T20223313010200010001211100100110011121110222020220\r\n",
"read_5447381\t0\tCGI_10003117\t357\t60\t48M\t*\t0\t0\tACCATTGAATCGATTTCCAAATGTGATGTTCCATCTGCAGTCCCTCTT\tB@B@BA?ABBAAABAABBA@5A@?@ABA>AAB@=?AB@?@7@@8@?@5\tNH:i:1\tCS:Z:T310130120323230020100311123110201322131212002220\r\n",
"read_5447382\t0\tCGI_10003117\t375\t60\t44M\t*\t0\t0\tAAATGTGATGTTCCATCTGCAGTCCCTCTTTAAATGGTCACAGT\t@?BB@@BABB>B@A??BBB9=B:B@@AAB<59>@><@>A?>?<:\tNH:i:1\tCS:Z:T30031112311020132213121200222003003101211121\r\n",
"read_5447383\t0\tCGI_10003117\t375\t60\t44M\t*\t0\t0\tAAATGTGATGTTCCATCTGCAGTCCCTCTTTAAATGGTCACAGT\t>@BB@?BBBA>@B>@<78?@=9@?A>>?;;\tNH:i:1\tCS:Z:T30031112311020132213121200222003003101211121\r\n",
"read_5447384\t0\tCGI_10003117\t375\t60\t44M\t*\t0\t0\tAAATGTGATGTTCCATCTGCAGTCCCTCTTTAAATGGTCACAGT\t@BB@@>@BAA=@@B?=B@B::@>5==?@@=/*?B81>;AA?@:7\tNH:i:1\tCS:Z:T30031112311020132213121200222003003101211121\r\n",
"read_5447385\t0\tCGI_10003117\t507\t60\t29M\t*\t0\t0\tGATGAATTGGTATAACATTGTCAACTCTT\tBBB?<@BBA=@BA?>=AA@;6@?<:8AA/\tNH:i:1\tCS:Z:T12312030101333011301121012220\r\n",
"read_5447386\t0\tCGI_10003117\t609\t60\t3S35M\t*\t0\t0\tAGCACAGATCCAAACTGGAATTTACCAGAACCGCCAGA\tBBBABBBABBBB>BA>@??BB@?AB@B<3@A>=9AA>=\tNH:i:1\tCS:Z:T32311122320100121020300310122010330122\r\n",
"read_5447387\t0\tCGI_10003117\t609\t60\t3S47M\t*\t0\t0\tAGCACAAATCCAAACTGGAATTTACCAGAACCGCCAGAAGAATACATCCC\tBBBABAA=BBBA@?B@=@?AB??BA?@<;A@:>=@>8:7@=><=@=<5;?\tNH:i:1\tCS:Z:T32311100320100121020300310122010330122022033113200\r\n",
"read_5447388\t0\tCGI_10003117\t609\t60\t3S35M\t*\t0\t0\tAGCACAGATCCAAACTGGAATTTACCAGAACCGCCAGA\tBBBBBBB@BBBBBB@B?BBBBB@BB@@==BA;A>AA@=\tNH:i:1\tCS:Z:T32311122320100121020300310122010330122\r\n",
"read_5447389\t0\tCGI_10003117\t609\t60\t48M2S\t*\t0\t0\tACAGATCCAAACTGGAATTTACCAGAACCGCCAGAAGAATACATCCCCCC\tBA@BBBBAB@BBAAB>ABB?BAA??>;=??>A>=97>@@AA537<;@=\tNH:i:1\tCS:Z:T31122320100121020300310122010330122022033113200000\r\n"
]
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#Lets figure out a way to visualize what genes are expressed\n",
"#Take RNA-seq file import into SQLShare\n",
"#imported /Volumes/web/cnidarian/solid0078_20091105_RobertsLab_GE_F3\\ trimmed\\ RNA-Seq.txt\n",
"#cleaned up\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 39
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
" \n",
"\n",
""
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#joining with annotation data.\n",
"#create generic SQLShare Wiki workflow.\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 42
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
" \n",
"--- "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/web/cnidarian/Cgigas_larvae_RNAseq_OsHV_GO.csv"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"ID,SPID1,GOID,term,aspect\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0003677,DNA binding,F\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0003700,transcription factor activity,F\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0005634,nucleus,C\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0005667,transcription factor complex,C\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0006351,\"\"\"transcription, DNA-dependent\"\"\",P\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0006355,\"\"\"regulation of transcription, DNA-dependent\"\"\",P\r",
"\r\n",
"CGI_10023548,A0AVK6,GO:0007049,cell cycle,P\r",
"\r\n",
"CGI_10003125,A0AVT1,GO:0000166,nucleotide binding,F\r",
"\r\n",
"CGI_10012444,A0AVT1,GO:0000166,nucleotide binding,F\r",
"\r\n"
]
}
],
"prompt_number": 43
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!wc /Volumes/web/cnidarian/Cgigas_larvae_RNAseq_OsHV_GO.csv"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
" 121979 315335 6935565 /Volumes/web/cnidarian/Cgigas_larvae_RNAseq_OsHV_GO.csv\r\n"
]
}
],
"prompt_number": 44
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"#into GoCategorizer then ManyEyes"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 45
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###Enrichment Analysis\n",
"\n",
"Background - all SPIDs associated with oyster transcriptome\n",
"Gene list - SPID of gene with at least 10 unique reads\n",
"\n",
"Kegg \n",
"\n",
"\n",
"\n",
"\n",
"\n",
"---\n",
"BP-Fat \n",
"\n",
"\n",
" \n",
" \n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"pvalue <.05 into Revigo"
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"GO:0008104\t1.87E-10\n",
"GO:0045184\t4.06E-10\n",
"GO:0015031\t1.55E-09\n",
"GO:0051056\t2.29E-08\n",
"GO:0046578\t7.92E-07\n",
"GO:0046907\t1.69E-06\n",
"GO:0006796\t8.93E-06\n",
"GO:0016310\t9.71E-06\n",
"GO:0006793\t1.68E-05\n",
"GO:0006396\t1.80E-05\n",
"GO:0016071\t2.05E-05\n",
"GO:0006886\t9.38E-05\n",
"GO:0043087\t3.10E-04\n",
"GO:0006468\t3.15E-04\n",
"GO:0034613\t3.40E-04\n",
"GO:0006511\t4.70E-04\n",
"GO:0006397\t4.72E-04\n",
"GO:0070727\t4.87E-04\n",
"GO:0006091\t5.48E-04\n",
"GO:0008380\t0.001634341\n",
"GO:0007049\t0.001856279\n",
"GO:0032318\t0.001879989\n",
"GO:0035023\t0.002340023\n",
"GO:0046034\t0.002847324\n",
"GO:0006644\t0.002942199\n",
"GO:0007017\t0.003300719\n",
"GO:0032313\t0.003409026\n",
"GO:0032483\t0.003409026\n",
"GO:0051169\t0.003795828\n",
"GO:0019637\t0.003832318\n",
"GO:0006913\t0.004482562\n",
"GO:0006412\t0.005141395\n",
"GO:0016568\t0.005563156\n",
"GO:0050657\t0.006346393\n",
"GO:0050658\t0.006346393\n",
"GO:0051236\t0.006346393\n",
"GO:0016265\t0.006480115\n",
"GO:0007010\t0.007213165\n",
"GO:0009141\t0.007619486\n",
"GO:0008219\t0.007723643\n",
"GO:0009142\t0.008393563\n",
"GO:0009057\t0.008477453\n",
"GO:0006818\t0.008580567\n",
"GO:0043954\t0.009700576\n",
"GO:0006325\t0.009965083\n",
"GO:0009205\t0.010315383\n",
"GO:0009199\t0.010315383\n",
"GO:0009145\t0.010315719\n",
"GO:0009206\t0.010315719\n",
"GO:0009201\t0.010315719\n",
"GO:0044265\t0.010376148\n",
"GO:0015992\t0.010857381\n",
"GO:0006403\t0.011334734\n",
"GO:0012501\t0.012741549\n",
"GO:0006754\t0.013504604\n",
"GO:0009894\t0.013504604\n",
"GO:0051301\t0.014127469\n",
"GO:0046486\t0.01575266\n",
"GO:0006650\t0.01589459\n",
"GO:0009165\t0.016043426\n",
"GO:0043632\t0.016123335\n",
"GO:0019941\t0.016123335\n",
"GO:0034330\t0.016219917\n",
"GO:0015986\t0.016219917\n",
"GO:0015985\t0.016219917\n",
"GO:0045494\t0.016219917\n",
"GO:0022613\t0.016633231\n",
"GO:0006119\t0.016730696\n",
"GO:0034622\t0.016780957\n",
"GO:0006915\t0.016867222\n",
"GO:0009144\t0.018450072\n",
"GO:0051028\t0.018450072\n",
"GO:0022618\t0.018899413\n",
"GO:0007265\t0.02172187\n",
"GO:0015931\t0.021879897\n",
"GO:0006163\t0.022368298\n",
"GO:0000278\t0.02349573\n",
"GO:0009150\t0.024939324\n",
"GO:0016192\t0.025101667\n",
"GO:0008203\t0.025445341\n",
"GO:0006413\t0.025494209\n",
"GO:0034504\t0.025886646\n",
"GO:0046822\t0.027243792\n",
"GO:0001701\t0.027310746\n",
"GO:0030163\t0.028215019\n",
"GO:0016042\t0.028610538\n",
"GO:0048193\t0.02882247\n",
"GO:0007163\t0.029465914\n",
"GO:0009259\t0.032187365\n",
"GO:0044257\t0.032802252\n",
"GO:0017038\t0.033241064\n",
"GO:0006164\t0.0341163\n",
"GO:0006605\t0.034586659\n",
"GO:0051603\t0.034854969\n",
"GO:0006401\t0.035288451\n",
"GO:0030031\t0.035977875\n",
"GO:0034621\t0.038678526\n",
"GO:0055085\t0.040014925\n",
"GO:0007018\t0.042241787\n",
"GO:0051170\t0.042255571\n",
"GO:0009311\t0.042515336\n",
"GO:0016579\t0.044317708\n",
"GO:0070646\t0.044317708\n",
"GO:0051276\t0.045536962\n",
"GO:0034654\t0.045690801\n",
"GO:0034404\t0.045690801\n",
"GO:0000226\t0.046104738\n",
"GO:0000375\t0.0482382\n",
"GO:0043161\t0.049498849\n",
"GO:0010498\t0.049498849"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"R script for treemap\n",
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"mm"
]
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"iPath"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"--- \n",
"###Mapping to OsHV\n",
"\n",
" \n",
"imported genbank format to hav CDS, gene information.. \n",
"started in CLC using same parameters..\n",
" \n",
" Minimum number of reads = 10\n",
" Minimum exon coverage fraction = 0.2\n",
" Additional downstream bases = 0\n",
" Use colorspace encoding = Yes\n",
" Create report = Yes\n",
" Use strand specific assembly = No\n",
" Count paired reads as two = No\n",
" Minimum length fraction (long reads) = 0.9\n",
" Additional upstream bases = 0\n",
" Unspecific match limit = 5\n",
" Expression value = RPKM\n",
" Minimum read count fusion gene table = 5\n",
" Create fusion gene table = No\n",
" Minimum paired distance = 180\n",
" Use annotations for gene and transcript identification = Yes\n",
" Strand = Forward\n",
" Organism type = PROKARYOTE\n",
" Maximum number of mismatches allowed (applies to short reads) = 2\n",
" Minimum similarity fraction = 0.8\n",
" References = NC_005881\n",
" Expression level = Genes\n",
" Minimum length of putative exons = 25\n",
" Maximum paired distance = 250\n",
" Create list of unmapped reads = No\n",
" Exon discovery = No\n",
" Expression value = Read Per Kilobase of exon Model value\n",
" \n",
"---\n",
"`\n",
"Found: 127 genes.\n",
"Total number of reads : 21344598 ( single reads: 21344598, paired reads: 0 )\n",
"Total number of mapped reads : 21135 ( single reads: 21135, paired reads: 0 )\n",
"Total number of unmapped reads : 21323463 ( single reads: 21323463, paired reads: 0 )\n",
"` \n",
" \n",
"\n",
" \n",
" \n",
"---\n",
" \n",
" \n",
" \n",
" \n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/web/cnidarian/solid0078_20091105_RobertsLab_GE_F3trim_RNAseqOSHV.csv"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\"Feature ID\",\"Expression values\",\"Gene length\",\"Unique gene reads\",\"Total gene reads\",\"RPKM\",\"Chromosome region start\",\"Chromosome region end\"\r\n",
"\"OsHV1_gp001\",\"423.399\",\"447\",\"0\",\"4\",\"423.399\",\"115\",\"561\"\r\n",
"\"OsHV1_gp002\",\"751.03\",\"504\",\"0\",\"8\",\"751.03\",\"680\",\"1183\"\r\n",
"\"OsHV1_gp003\",\"61.85\",\"765\",\"0\",\"1\",\"61.85\",\"1890\",\"2654\"\r\n",
"\"OsHV1_gp004\",\"2748.769\",\"1050\",\"0\",\"61\",\"2748.769\",\"3384\",\"4433\"\r\n",
"\"OsHV1_gp005\",\"3168.303\",\"2031\",\"70\",\"136\",\"3168.303\",\"6421\",\"8451\"\r\n",
"\"OsHV1_gp006\",\"1534.465\",\"3546\",\"115\",\"115\",\"1534.465\",\"8628\",\"12173\"\r\n",
"\"OsHV1_gp007\",\"1429.304\",\"960\",\"29\",\"29\",\"1429.304\",\"12211\",\"13170\"\r\n",
"\"OsHV1_gp008\",\"4016.047\",\"1779\",\"151\",\"151\",\"4016.047\",\"13258\",\"15036\"\r\n",
"\"OsHV1_gp009\",\"6345.436\",\"1029\",\"138\",\"138\",\"6345.436\",\"15297\",\"16325\"\r\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"### Reference Mapping to OsHV\n",
" \n",
" \n",
"\n",
"\n",
"\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"SAM file "
]
},
{
"cell_type": "heading",
"level": 3,
"metadata": {},
"source": [
"SNP ID based on Reference Mapping"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!cat /Volumes/web/cnidarian/OsHV_snp_table"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\"Reference Position\"\t\"Type\"\t\"Length\"\t\"Reference\"\t\"Allele\"\t\"Linkage\"\t\"Zygosity\"\t\"Count\"\t\"Coverage\"\t\"Frequency\"\t\"Forward/reverse balance\"\t\"Average quality\"\t\"Overlapping annotations\"\t\"Coding region change\"\t\"Amino acid change\"\r\n",
"32003\tSNV\t1\tG\tA\t\tHomozygous\t12\t12\t100\t0.417\t23.833\tGene: OsHV1_gp021, CDS: OsHV1_gp021, Misc. feature: UL\tYP_024567.1:c.1533G>A\tYP_024567.1:p.Met511Ile\r\n",
"57377\tSNV\t1\tC\tT\t\tHomozygous\t10\t10\t100\t0.1\t24.1\tGene: OsHV1_gp039, CDS: OsHV1_gp039, Misc. feature: UL\tYP_024585.1:c.1468C>T\tYP_024585.1:p.Pro490Ser\r\n",
"83889\tSNV\t1\tA\tG\t\tHomozygous\t18\t18\t100\t0.056\t27.222\tGene: OsHV1_gp053, CDS: OsHV1_gp053, Misc. feature: UL\tYP_024599.1:c.554A>G\tYP_024599.1:p.Glu185Gly\r\n",
"92644\tSNV\t1\tA\tG\t\tHomozygous\t13\t13\t100\t0.462\t23.769\tGene: OsHV1_gp058, CDS: OsHV1_gp058, Misc. feature: UL\tYP_024604.1:c.1349A>G\tYP_024604.1:p.Tyr450Cys\r\n",
"124796\tSNV\t1\tG\tA\t\tHomozygous\t10\t10\t100\t0.1\t30.2\tGene: OsHV1_gp071, CDS: OsHV1_gp071, Misc. feature: UL\tYP_024617.1:c.2083G>A\tYP_024617.1:p.Ala695Thr\r\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"##IGV Browser for OsHV"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/web/cnidarian/solid0078_20091105_RbbertsLab_GE_F3\\ trimmed\\ mapping.sam"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"@HD\tVN:1.0\tSO:unsorted\r\n",
"@SQ\tSN:NC_005881\tLN:207439\tSP:Ostreid herpesvirus 1\r\n",
"@PG\tID:0\tPN:clcgenomicswb\tVN:7.0\r\n",
"read_1\t0\tNC_005881\t2764\t60\t2S18M\t*\t0\t0\tCATGGGGGGGGGGGGGGGGG\tBB@??979/12.=<+9-;22\tNH:i:1\tCS:Z:T21312000000000000000\r\n",
"read_2\t16\tNC_005881\t7624\t60\t32M\t*\t0\t0\tCACTTGACAACATCCATACATATCGTCATCCA\t>9;3,@5>/<@7?=8BA>B:B?A<=@AA;7B@\tNH:i:1\tCS:Z:T01023121323331133102311011200211\r\n",
"read_3\t16\tNC_005881\t7624\t60\t26M\t*\t0\t0\tCACTTGACAACATCCATACATATCGT\t?>;>2?5>?>BBBBABB\tNH:i:1\tCS:Z:T31323331133102311011210211\r\n",
"read_4\t16\tNC_005881\t7638\t60\t46M\t*\t0\t0\tCATACATATCGTCATCCAGGGTCTCTCCGTGTTTAGGATATAGCGT\t0=??6&A8:?9>>>@9??>@@B6@ABBA?ABBBB>BBBBBAB\tNH:i:1\tCS:Z:T3133233332023001113022222100210231211233311331\r\n",
"read_5\t0\tNC_005881\t7640\t60\t34M\t*\t0\t0\tTACATATCGTCATCCAGGGTCTCTCCGTGTTTAG\tBBAABBBBBABBBBABBBBAB@BB@BBA@+>BBB\tNH:i:1\tCS:Z:T0311333231213201200122222031110032\r\n",
"read_6\t16\tNC_005881\t7640\t60\t44M\t*\t0\t0\tTACATATCGTCATCCAGGGTCTCTCCGTGTTTAGGATATAGCGT\t=26?+:0/:04;=87232=1-1ABA+@BB?%B@B;??6B>\tNH:i:1\tCS:Z:T0311333231213201200122222031110032023333233133333\r\n"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!head /Volumes/web/cnidarian/NC_005881"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
">NC_005881 Ostreid herpesvirus 1, complete genome.\r\n",
"CCCCCCACCTCCCCAACACCTCCCCCATCCTCCCCACCTCCTCCCCCTCCTCTCTTCCGC\r\n",
"CCGCGATCCCGCCAATACCCATAATGCACCTGGGCACTCTCTTTTTTCCTTTCCTTATCC\r\n",
"AAGATGTCCGCCCATTGCCAGGTACAGCCTTCCCACCGTGTGAACAATGTCCATCCTCTT\r\n",
"CTCCGAGACTTCCCTGACCAGATTGTCGTAATCCAATTGACACATTCTCGTCAATGCCCT\r\n",
"CCTCATATTCTCCATCGGCCAACTGTCGTCTCTACTCATGGTCATAAACAATCCCAATCC\r\n",
"ACTCTTGGCATCCCGCAACCTTTCCAATAGCCTCCCGAATTCGTCTACCGCCGCCTTATC\r\n",
"GTCGTCCGTGCTGCAATGTGGTCTTACCGCATTTTTAAGCAATGCGCACGCCACTCTCAA\r\n",
"TTCCTGACAGGTAATCTCCTCCACCGGTTTCCTATCGTGTAATAGACTGACCACGGCGGC\r\n",
"CATGTCTCTCAGTTCCTTGCTCATCTCACCACCGCCAACCAATTCAGCAGTGACAGTTAC\r\n"
]
}
],
"prompt_number": 7
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"LINKOUT to xml `http://eagle.fish.washington.edu/cnidarian/OsHV_igv_session.xml`"
]
},
{
"cell_type": "heading",
"level": 3,
"metadata": {},
"source": [
"Mapping to GQ153938"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}