{ "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": [ "\"greenbird_196B0D35.png\"/" ] }, { "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", "\"File_196B2C85.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "4) Enter `http://eagle.fish.washington.edu/cnidarian/igv_session_YElarvae.xml` \n", "\n", "\"Screenshot_7_7_14__12_30_PM_196B2CE2.png\"/" ] }, { "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", " \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": {} } ] }