{ "metadata": { "name": "TJGR_OysterGenome_IGV" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": "#Developing Canonical Tracks for IGV Oyster Genome Browser" }, { "cell_type": "markdown", "metadata": {}, "source": "This is my attempt derive fundamental genomic tracks for the oyster genome that can be easily visualized. \nLast Updated: **June 01, 2013**\n\nContents \n\n- [Launching IGV](#IGV)\n- [Loading CDS and mRNA tracks](#cds)\n- [Gill Tissue Methylation](#gillmeth)\n- [Sperm Methylation](#spermmeth)\n- [Gill and Sperm gene level expression - RPKM](#rpkm)\n\n\n
" }, { "cell_type": "markdown", "metadata": {}, "source": "Will use the full genome as scaffold (should be in cnidaria)" }, { "cell_type": "markdown", "metadata": {}, "source": "###Launching Integrative Genome Viewer" }, { "cell_type": "markdown", "metadata": {}, "source": "_Launch IGV_\n\nclicking this file opens the app\n\n\"Screenshot%205/27/13%2012:14%20PM\"\n\n###Load genome via url\n\n\"Screenshot%205/27/13%2012:16%20PM\"\n\n###Load CDS and mRNA GFF\n\n\n \n\n \n
\n\"Screenshot%205/27/13%2012:22%20PM\"" }, { "cell_type": "markdown", "metadata": {}, "source": "
\n###Gill Methylation - MBD BS-Seq data\n\nmethratio did produce output and his was uploaded to SQLShare\n\n\"Screenshot%205/27/13%2012:27%20PM\"\n\n
\nhttps://sqlshare.escience.washington.edu/sqlshare#s=query/sr320%40washington.edu/BiGill_methratio_v9_A.txt\n
\n\"Screenshot%205/27/13%2012:31%20PM\"\n
\n_converted to GFF format_ [see example](https://github.com/uwescience/sqlshare/wiki/Workflow:-Analysis-of-BSMAP-data#how-to-convert-methratio-file-to-gff-format)\n
\n_resulting file_\n\n\n" }, { "cell_type": "raw", "metadata": {}, "source": "IGV session file available:\nhttp://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml" }, { "cell_type": "markdown", "metadata": {}, "source": "
" }, { "cell_type": "markdown", "metadata": {}, "source": "Want to convert to IGV\n\n\"Screenshot%205/28/13%208:53%20PM\"" }, { "cell_type": "markdown", "metadata": {}, "source": "\n SELECT \n chr as seqname, \n pos - 1 as start, -- compensating for going to zero-based?\n pos + 1 as [end], \n 'CG' as feature, \n ratio as score \n\n FROM [sr320@washington.edu]. \n [BiGill_methratio_v9_A.txt] yel \n where \n context like '__CG_' --_=single character wildcard\n and\n CT_Count >= 5\u200b\n" }, { "cell_type": "markdown", "metadata": {}, "source": "---\n python fetchdata.py -d \"[sr320@washington.edu].[BiGill_methratio_v9_IGV]\u200b\u200b\u200b\" -f tsv -o /Volumes/web/cnidarian/BiGill_meth_v9_5x.igv" }, { "cell_type": "code", "collapsed": false, "input": "!head /Volumes/web/cnidarian/BiGill_meth_v9_5x.igv", "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": "seqname\tstart\tend\tfeature\tscore\r\r\nC10009\t69\t71\tCG\t0.000\r\r\nC10049\t42\t44\tCG\t0.200\r\r\nC10049\t51\t53\tCG\t0.071\r\r\nC10075\t86\t88\tCG\t0.200\r\r\nC1009\t88\t90\tCG\t0.833\r\r\nC10093\t106\t108\tCG\t0.875\r\r\nC10107\t27\t29\tCG\t0.000\r\r\nC10107\t92\t94\tCG\t0.667\r\r\nC10127\t71\t73\tCG\t0.000\r\r\n" } ], "prompt_number": 4 }, { "cell_type": "markdown", "metadata": {}, "source": "Imported in IGV and looks like coordinates are ok" }, { "cell_type": "markdown", "metadata": {}, "source": "\"Screenshot%205/28/13%209:11%20PM\"" }, { "cell_type": "markdown", "metadata": {}, "source": "
\n\"Screenshot%205/28/13%209:13%20PM\"" }, { "cell_type": "markdown", "metadata": {}, "source": "
\n### Male Gonad Methylation data\nDeveloping IGV file format" }, { "cell_type": "markdown", "metadata": {}, "source": "\n SELECT \n chr as seqname, \n pos - 1 as start, -- compensating for going to zero-based?\n pos + 1 as [end], \n 'CG' as feature, \n ratio as score \n\n FROM [sr320@washington.edu]. \n [BiGO_betty_plain_methratio_v1.txt] yel \n where \n context like '__CG_' --_=single character wildcard\n and\n CT_Count >= 5\u200b\n" }, { "cell_type": "markdown", "metadata": {}, "source": "--- \n python fetchdata.py -d \"[sr320@washington.edu].[BiGO_betty_methratio_v1_IGV]\u200b\u200b\u200b\" -f tsv -o /Volumes/web/cnidarian/BiGO_betty_methratio_v1.igv\n" }, { "cell_type": "markdown", "metadata": {}, "source": "" }, { "cell_type": "markdown", "metadata": {}, "source": "\"Screenshot%205/29/13%204:01%20PM\"" }, { "cell_type": "markdown", "metadata": {}, "source": "IGV Session resaved\nhttp://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml\n\n*Details on sperm exon level expression available [here](http://nbviewer.ipython.org/url/eagle.fish.washington.edu/cnidarian/TJGR_Mgo_Expression.ipynb)*\n\n\n\n" }, { "cell_type": "markdown", "metadata": {}, "source": "
\n### Adding gene level expresssion for sperm and gill" }, { "cell_type": "markdown", "metadata": {}, "source": "Gene level expression is in SQLShare, originally derived from CLC RNA-Seq" }, { "cell_type": "markdown", "metadata": {}, "source": "**Gill Expression data**\n\n\n\n\"Screenshot%206/2/13%208:14%20AM\"\n \n_SQLShare Query_\n \n \n SELECT \n Chromosome,\n \"Chromosome region start\" - 1 as start,\n \"Chromosome region end\" as [end],\n 'gene' as feature,\n RPKM \n \n FROM [sr320@washington.edu].[qDOD_Zhang_Gil_gene_RNA-seq]\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\u200b\n \n_Resulting file_\n\n \n_Downloading_ \n `python fetchdata.py -d \"[sr320@washington.edu].[Zhang_Gil_gene_RNA-seq_IGV]\u200b\" -f tsv -o /Volumes/web/cnidarian/Zhang_Gil_gene_RNA-seq.igv`\n \n_Needs to be sorted in IGV_ \n \n " }, { "cell_type": "markdown", "metadata": {}, "source": "**Sperm Gene level expression**\n\nFile in SQLShare \n\n_SQLShare Query_ \n```\nSELECT \nChromosome,\n\"Chromosome region start\" - 1 as start,\n\"Chromosome region end\" as [end],\n'gene' as feature,\nRPKM as Mgo_RPKM\nFROM [sr320@washington.edu].[qDOD_Zhang_Mgo_gene_RNA-seq]\u200b\n```\n\n_New Dataset_\n\n \n_Downloading_ \n`python fetchdata.py -d \"[sr320@washington.edu].[Zhang_Mgo_gene_RNA-seq_IGV]\u200b\u200b\" -f tsv -o /Volumes/web/cnidarian/Zhang_Mgo_gene_RNA-seq.igv `\n \n_Sorted_ \n\n\n
\nNew IGV Browser ...\n\n\"Screenshot%206/2/13%209:48%20AM\" \nhttp://eagle.fish.washington.edu/cnidarian/oyster_v9_igv_session.xml\n \n" }, { "cell_type": "code", "collapsed": false, "input": "", "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }