deletions | additions       diff --git a/ipynb/.ipynb_checkpoints/Array-feature-overlap-04-checkpoint.ipynb b/ipynb/.ipynb_checkpoints/Array-feature-overlap-04-checkpoint.ipynb  new file mode 100644  index 0000000..1329c62  --- /dev/null  +++ b/ipynb/.ipynb_checkpoints/Array-feature-overlap-04-checkpoint.ipynb 
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{  "cells": [  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# Intersect bed on gene-centric features"  ]  },  {  "cell_type": "code",  "execution_count": 3,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  "Fri Mar 13 08:02:12 PDT 2015\r\n"  ]  }  ],  "source": [  "!date"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "Feature (from nb -03) \n",  "\n",  "**tldr** 4 \"new\" tracks\n",  "\n",  "```\n",  "/Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf\n",  "/Users/sr320/data-genomic/tentacle/rebuilt.gtf\n",  "/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-housekeeping.gff\n",  "/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-env-response.gff\n",  "```"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# DEGs"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "`-wb\tWrite the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.`"  ]  },  {  "cell_type": "code",  "execution_count": 6,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 880 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 7,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 704 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 8,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 632 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 10,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  "117460 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/array-design/OID40453_probe_locations.gff \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 11 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# Rebuilt (new gtf based on RNAseq data)"  ]  },  {  "cell_type": "code",  "execution_count": null,  "metadata": {  "collapsed": true  },  "outputs": [],  "source": []  }  ],  "metadata": {  "kernelspec": {  "display_name": "Python 2",  "language": "python",  "name": "python2"  },  "language_info": {  "codemirror_mode": {  "name": "ipython",  "version": 2  },  "file_extension": ".py",  "mimetype": "text/x-python",  "name": "python",  "nbconvert_exporter": "python",  "pygments_lexer": "ipython2",  "version": "2.7.9"  }  },  "nbformat": 4,  "nbformat_minor": 0  }  diff --git a/ipynb/Array-feature-overlap-04.ipynb b/ipynb/Array-feature-overlap-04.ipynb  new file mode 100644  index 0000000..1329c62  --- /dev/null  +++ b/ipynb/Array-feature-overlap-04.ipynb 
...
{  "cells": [  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# Intersect bed on gene-centric features"  ]  },  {  "cell_type": "code",  "execution_count": 3,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  "Fri Mar 13 08:02:12 PDT 2015\r\n"  ]  }  ],  "source": [  "!date"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "Feature (from nb -03) \n",  "\n",  "**tldr** 4 \"new\" tracks\n",  "\n",  "```\n",  "/Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf\n",  "/Users/sr320/data-genomic/tentacle/rebuilt.gtf\n",  "/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-housekeeping.gff\n",  "/Users/sr320/data-genomic/tentacle/Cgigas_v9_gene-env-response.gff\n",  "```"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# DEGs"  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "`-wb\tWrite the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.`"  ]  },  {  "cell_type": "code",  "execution_count": 6,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 880 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.2M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 7,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 704 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.4M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 8,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  " 632 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a ./data/2014.07.02.colson/genomeBrowserTracks/logFC_HS-preHS/2014.07.02.6M_sig.bedGraph \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 6 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "code",  "execution_count": 10,  "metadata": {  "collapsed": false  },  "outputs": [  {  "name": "stdout",  "output_type": "stream",  "text": [  "117460 Cufflinks\r\n"  ]  }  ],  "source": [  "!intersectbed \\\n",  "-wb \\\n",  "-a /Users/sr320/git-repos/paper-Temp-stress/ipynb/data/array-design/OID40453_probe_locations.gff \\\n",  "-b /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf \\\n",  "| cut -f 11 \\\n",  "| sort | uniq -c "  ]  },  {  "cell_type": "markdown",  "metadata": {},  "source": [  "# Rebuilt (new gtf based on RNAseq data)"  ]  },  {  "cell_type": "code",  "execution_count": null,  "metadata": {  "collapsed": true  },  "outputs": [],  "source": []  }  ],  "metadata": {  "kernelspec": {  "display_name": "Python 2",  "language": "python",  "name": "python2"  },  "language_info": {  "codemirror_mode": {  "name": "ipython",  "version": 2  },  "file_extension": ".py",  "mimetype": "text/x-python",  "name": "python",  "nbconvert_exporter": "python",  "pygments_lexer": "ipython2",  "version": "2.7.9"  }  },  "nbformat": 4,  "nbformat_minor": 0  }