AmpliconArchitect_reconstructions.tar.gz (55.02 MB)
AmpliconArchitect_reconstructions
Version 2 2018-03-09, 00:35
Version 1 2018-03-08, 15:03
dataset
posted on 2018-03-09, 00:35 authored by Viraj DeshpandeViraj DeshpandeThis dataset contains the AmpliconArchitect (https://github.com/virajbdeshpande/AmpliconArchitect) output for reconstruction of amplicons from the following samples:
1) 117 samples in "sample set 1" https://www.ncbi.nlm.nih.gov/bioproject/PRJNA338012/
2) 18 samples which replicates of samples in sample set 1
3) 67 cervical samples from TCGA with HPV infection
4) Amplicons from sample set 1 organized by various tags including: a) MultCluster, b) MultiChrom c) simple_cycles and d) BFB
5) 7 samples reported by L'abbate et al 2014
6) 3 samples reported by Sanborn et al 2013 + 1 sample reported by Oesper et al 2012
7) 9 samples reported by Akagi et al 2013.
1 summary file for each sample:
_summary.txt - Summary of all amplicons reported in the sample.
4 files per amplicon:
graph.txt file: Breakpoint graph and copy numbers
cycles.txt file: Simple cycles in amplicon
.png and .pdf: SV view of reconstruction.
For viral amplicons from (3) and (7), 2 additional files (png and pdf) for each human interval connected to the viral genome.
.png and .cycles.txt files may be uploaded to http://genomequery.ucsd.edu:8800 for visualization and merging of cycles
