{
"metadata": {
"name": "",
"signature": "sha256:554981b186a25aeb2a2eb7d4c3753e53a5a73502ec9b609d59f46c7651588442"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Yanouk's samples - Hypo and Hypermethylated loci (3x)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
"Instructions for Visualization"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"1) Install IGV (free software) http://www.broadinstitute.org/software/igv/home"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"from IPython.display import HTML\n",
"HTML('')\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"html": [
""
],
"metadata": {},
"output_type": "pyout",
"prompt_number": 4,
"text": [
""
]
}
],
"prompt_number": 4
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"2) Open IGV"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"3) Go to File > Load from URL... \n",
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"4) Enter `http://eagle.fish.washington.edu/cnidarian/igv_session_YElarvae.xml` \n",
"\n",
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Voila- you should get a window similar to the what is at the top of the page.\n",
"\n",
"Tracks include\n",
"methylation data at 3x and 5x coverage and a track representing loci that are hypermethylated in mix library and hypomethylated in mix sample.\n",
"\n",
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"IGV xml to directly load all tracks above\n",
"\n",
"http://eagle.fish.washington.edu/cnidarian/igv_session_YElarvae.xml"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"!cat /Volumes/web/cnidarian/igv_session_YElarvae.xml"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\r\n",
"\r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
" \r\n",
"\r\n"
]
}
],
"prompt_number": 12
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Adding some larvae RNA-seq Tracks"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"bgdir=\"/iplant/home/sr320/Cgigas_v9/Zhang/bgraph\"\n",
"!ils {bgdir}"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/iplant/home/sr320/Cgigas_v9/Zhang/bgraph:\r\n"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_E-2014-03-08-07-36-07.971\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_early-2014-07-08-09-17-15.654\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_Fgo-2014-03-07-10-07-12.617\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_G3-2014-03-06-16-26-41.026\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_late-2014-07-08-09-15-42.258\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_Man1-2014-07-02-08-36-42.069\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_Mgo1.3-2014-03-07-14-06-07.430\r\n",
" C- /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/RNAseq2bedgraph_Mgo-2014-03-07-14-03-33.677\r\n"
]
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"folder=\"RNAseq2bedgraph_late-2014-07-08-09-15-42.258\"\n",
"id=\"late\""
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cd /Volumes/web/cnidarian/\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"/Volumes/web/cnidarian\n"
]
}
],
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": true,
"input": [
"!icd /iplant/home/sr320/Cgigas_v9/Zhang/bgraph/{folder}\n",
"!imv accepted_hits.bam z{id}_tophat.bam\n",
"!imv bedtools_genomecov_output z{id}_th_genomecov.bedgraph\n",
"!iget -f z{id}_th_genomecov.bedgraph\n",
"!iget -f z{id}_tophat.bam\n",
"!igvtools toTDF z{id}_th_genomecov.bedgraph z{id}_th_genomecov.bedgraph.tdf /Volumes/web/cnidarian/cgigas_v9_genome03.chrom.sizes \n",
"!iput z{id}_th_genomecov.bedgraph.tdf"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}