deletions | additions       diff --git a/ipynb/RNA-seq-Gene-ID.ipynb b/ipynb/RNA-seq-Gene-ID.ipynb  index 76201ae..67cf622 100644  --- a/ipynb/RNA-seq-Gene-ID.ipynb  +++ b/ipynb/RNA-seq-Gene-ID.ipynb 
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"Product GTF of ONLY Diffexp genes"  ]  },  {  "cell_type": "code",  "collapsed": false,  "input": [  "!head /Users/sr320/data-genomic/tentacle/Cuffdiff_geneexp.sig.gtf"  ],  "language": "python",  "metadata": {},  "outputs": [  {  "output_type": "stream",  "stream": "stdout",  "text": [  "C17036\tCufflinks\texon\t245\t442\t.\t.\t.\tgene_id XLOC_000059; tss_id \"TSS59\"; oId \"CUFF.56.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000059\"\r",  "\r\n",  "C17036\tCufflinks\tCDS\t245\t442\t.\t.\t.\tgene_id XLOC_000059; tss_id \"TSS59\"; oId \"CUFF.56.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000059\"\r",  "\r\n",  "C18346\tCufflinks\texon\t174\t551\t.\t+\t.\tgene_id CGI_10000009; tss_id \"TSS114\"; nearest_ref \"EKC17950\"; exon_number \"1\"; class_code \"=\"; p_id \"P6\"; gene_name \"CGI_10000009\"; transcript_id \"EKC17950\"\r",  "\r\n",  "C18346\tCufflinks\tCDS\t174\t551\t.\t+\t.\tgene_id CGI_10000009; tss_id \"TSS114\"; nearest_ref \"EKC17950\"; exon_number \"1\"; class_code \"=\"; p_id \"P6\"; gene_name \"CGI_10000009\"; transcript_id \"EKC17950\"\r",  "\r\n",  "C18548\tCufflinks\texon\t1\t33\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t1\t33\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\texon\t300\t629\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"2\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18548\tCufflinks\tCDS\t300\t629\t.\t+\t.\tgene_id XLOC_000124; tss_id \"TSS124\"; oId \"CUFF.116.1\"; exon_number \"2\"; class_code \"u\"; transcript_id \"TCONS_00000124\"\r",  "\r\n",  "C18752\tCufflinks\texon\t2\t631\t.\t.\t.\tgene_id XLOC_000133; tss_id \"TSS133\"; oId \"CUFF.125.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000133\"\r",  "\r\n",  "C18752\tCufflinks\tCDS\t2\t631\t.\t.\t.\tgene_id XLOC_000133; tss_id \"TSS133\"; oId \"CUFF.125.1\"; exon_number \"1\"; class_code \"u\"; transcript_id \"TCONS_00000133\"\r",  "\r\n"  ]  }  ],  "prompt_number": 74  },  {  "cell_type": "code",  "collapsed": false,