deletions | additions       diff --git a/ipynb/RNA-seq-Gene-ID.ipynb b/ipynb/RNA-seq-Gene-ID.ipynb  index 67cf622..ea31a46 100644  --- a/ipynb/RNA-seq-Gene-ID.ipynb  +++ b/ipynb/RNA-seq-Gene-ID.ipynb 
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],  "prompt_number": 3  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!wc -l ./data/Cuffdiff2_heat-b-2014-12-20-22-27-15.4/sorted_data/genes.sorted_by_expression.sig.txt"  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  " 1551 ./data/Cuffdiff2_heat-b-2014-12-20-22-27-15.4/sorted_data/genes.sorted_by_expression.sig.txt\r\n"  ]  }  ],  "prompt_number": 4  },  {  "cell_type": "code",  "collapsed": false, 
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]  }  ],  "prompt_number": 11 2  },  {  "cell_type": "code", 
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"cell_type": "code",  "collapsed": false,  "input": [  "!head "!tail  /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf" ],  "language": "python",  "metadata": {}, 
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"output_type": "stream",  "stream": "stdout",  "text": [  "C17036\tCufflinks\texon\t245\t442\t.\t.\t.\tgene_id XLOC_000059; "scaffold99\tCufflinks\texon\t280996\t281077\t.\t-\t.\tgene_id CGI_10021197;  tss_id \"TSS59\"; oId \"CUFF.56.1\"; \"TSS54694\"; nearest_ref \"EKC41856\";  exon_number \"1\"; \"3\";  class_code \"u\"; \"j\"; gene_name \"CGI_10021197\";  transcript_id \"TCONS_00000059\"\r", \"CUFF.28727.2\"\r",  "\r\n",  "C17036\tCufflinks\tCDS\t245\t442\t.\t.\t.\tgene_id XLOC_000059; "scaffold99\tCufflinks\tCDS\t280996\t281077\t.\t-\t.\tgene_id CGI_10021197;  tss_id \"TSS59\"; oId \"CUFF.56.1\"; \"TSS54694\"; nearest_ref \"EKC41856\";  exon_number \"1\"; \"3\";  class_code \"u\"; \"j\"; gene_name \"CGI_10021197\";  transcript_id \"TCONS_00000059\"\r", \"CUFF.28727.2\"\r",  "\r\n",  "C18346\tCufflinks\texon\t174\t551\t.\t+\t.\tgene_id CGI_10000009; "scaffold99\tCufflinks\texon\t280996\t281100\t.\t-\t.\tgene_id CGI_10021197;  tss_id \"TSS114\"; \"TSS54694\";  nearest_ref \"EKC17950\"; \"EKC41856\";  exon_number \"1\"; \"3\";  class_code \"=\"; p_id \"P6\"; \"P26038\";  gene_name \"CGI_10000009\"; \"CGI_10021197\";  transcript_id \"EKC17950\"\r", \"EKC41856\"\r",  "\r\n",  "C18346\tCufflinks\tCDS\t174\t551\t.\t+\t.\tgene_id CGI_10000009; "scaffold99\tCufflinks\tCDS\t280996\t281100\t.\t-\t.\tgene_id CGI_10021197;  tss_id \"TSS114\"; \"TSS54694\";  nearest_ref \"EKC17950\"; \"EKC41856\";  exon_number \"1\"; \"3\";  class_code \"=\"; p_id \"P6\"; \"P26038\";  gene_name \"CGI_10000009\"; \"CGI_10021197\";  transcript_id \"EKC17950\"\r", \"EKC41856\"\r",  "\r\n",  "C18548\tCufflinks\texon\t1\t33\t.\t+\t.\tgene_id XLOC_000124; "scaffold992\tCufflinks\texon\t9014\t9344\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS124\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.116.1\"; \"CUFF.28745.1\";  exon_number \"1\"; class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000124\"\r", \"TCONS_00075736\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t1\t33\t.\t+\t.\tgene_id XLOC_000124; "scaffold992\tCufflinks\tCDS\t9014\t9344\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS124\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.116.1\"; \"CUFF.28745.1\";  exon_number \"1\"; class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000124\"\r", \"TCONS_00075736\"\r",  "\r\n",  "C18548\tCufflinks\texon\t300\t629\t.\t+\t.\tgene_id XLOC_000124; "scaffold992\tCufflinks\texon\t9669\t9825\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS124\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.116.1\"; \"CUFF.28745.1\";  exon_number \"2\"; class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000124\"\r", \"TCONS_00075736\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t300\t629\t.\t+\t.\tgene_id XLOC_000124; "scaffold992\tCufflinks\tCDS\t9669\t9825\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS124\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.116.1\"; \"CUFF.28745.1\";  exon_number \"2\"; class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000124\"\r", \"TCONS_00075736\"\r",  "\r\n",  "C18752\tCufflinks\texon\t2\t631\t.\t.\t.\tgene_id XLOC_000133; "scaffold992\tCufflinks\texon\t10327\t10415\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS133\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.125.1\"; \"CUFF.28745.1\";  exon_number \"1\"; \"3\";  class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000133\"\r", \"TCONS_00075736\"\r",  "\r\n",  "C18752\tCufflinks\tCDS\t2\t631\t.\t.\t.\tgene_id XLOC_000133; "scaffold992\tCufflinks\tCDS\t10327\t10415\t.\t+\t.\tgene_id XLOC_036046;  tss_id \"TSS133\"; \"TSS54716\"; nearest_ref \"EKC31279\";  oId \"CUFF.125.1\"; \"CUFF.28745.1\";  exon_number \"1\"; \"3\";  class_code \"u\"; \"x\"; gene_name \"CGI_10007500\";  transcript_id \"TCONS_00000133\"\r", \"TCONS_00075736\"\r",  "\r\n"  ]  }  ],  "prompt_number": 74 4  },  {  "cell_type": "code",