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    "### extract allelic raed counts from TCGA RNAseq and WXS bams\n",
    "\n",
    "| Description | Location           | \n",
    "| ------------- | :------|\n",
    "|identify relevant TCGA WXS and RNAseq|http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/identify_TCGA_WGS_runs.ipynb |\n",
    "| | |"
   ]
  },
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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#  allelic fraction extraction in TCGA pipeline\n",
    "\n",
    "| input        |output| Location           | \n",
    "| ------------- |:-------------:| \n",
    "| raw bams from TCGA website     |allelic read counts| http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/submitJobForAllleleExtraction.ipynb |\n",
    "|TCGA website| preprocessed TCGA VCF files| http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/downloadingVCFs.ipynb|\n",
    "|TCGA website| VCF metadata annotations| http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Pull_TCGA_meta_data.ipynb|\n",
    "|preprocessed TCGA VCF files| merged VCF file| http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/mergeTCGA_VCF.ipynb#|\n",
    "|reprocessed bam-reacount out files| merged bam-reacount out file|http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/mergeBamReadCountFiles.ipynb\n",
    "\n",
    "# analysis\n",
    "| Description| Location           | \n",
    "| ------------- |:-------------:| \n",
    "|calling mutation in TCGA using simple allelic read counts with less than 10 lines|http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/mutationCalling.ipynb#|\n",
    "|analyze RNA-seq and WXS allelic read count concordance | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Compare_TCGA_RNAseq_WXS.ipynb |\n",
    "\n",
    "The URL locations are hardcoded for me clicking to go to different notebooks. \n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# scratch\n",
    "\n",
    "Find TCGA WXS runs\n",
    "http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/identify_TCGA_WGS_runs.ipynb\n",
    "\n",
    "check for TCGA aligning speed: \n",
    "\n",
    "http://localhost:6001/edit/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/align_tcga.py"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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