2018-03-09T00:35:22Z (GMT) by Viraj Deshpande
This dataset contains the AmpliconArchitect ( output for reconstruction of amplicons from the following samples:<div><br></div><div>1) 117 samples in "sample set 1"<div><br></div><div>2) 18 samples which replicates of samples in sample set 1</div><div><br></div><div>3) 67 cervical samples from TCGA with HPV infection</div><div><br></div><div>4) Amplicons from sample set 1 organized by various tags including: a) MultCluster, b) MultiChrom c) simple_cycles and d) BFB</div><div><br></div><div>5) 7 samples reported by L'abbate et al 2014</div><div><br></div><div>6) 3 samples reported by Sanborn et al 2013 + 1 sample reported by Oesper et al 2012</div><div><br></div><div>7) 9 samples reported by Akagi et al 2013.</div><div><br></div><div>1 summary file for each sample:</div><div>_summary.txt - Summary of all amplicons reported in the sample.</div><div><br></div><div>4 files per amplicon:</div><div>graph.txt file: Breakpoint graph and copy numbers</div><div>cycles.txt file: Simple cycles in amplicon</div><div>.png and .pdf: SV view of reconstruction.</div><div><br></div><div>For viral amplicons from (3) and (7), 2 additional files (png and pdf) for each human interval connected to the viral genome.</div><div><br></div><div>.png and .cycles.txt files may be uploaded to for visualization and merging of cycles</div></div>