High-throughput genome scaffolding from in vivo DNA interaction frequency

Noam Kaplan & Job Dekker

Nature Biotechnology 31: 1143-1147. (2013)

full text

Supplementary data

Dixon12_hESC-R2A_hg19all_huref.tab.gz (Hi-C interaction matrix)
Data: Sampled one third of h1 hESC Hi-C data produced by Dixon et al., 2012. 50% of reads from replicate 2 (~33% of data) were used, in total ~248M reads.
Genome: mapped to hg19 + hg19 unplaced contigs + HuRef unplaced contigs
Format: chr_or_contig_id[tab]bin_start[tab]bin_end[tab]data_i_1[tab]data_i_2[tab]...[tab]data_i_n

Dixon12_hESC-AllpathsLGcontigs.tab.gz (Hi-C interaction matrix)
Data: h1 hESC Hi-C data produced by Dixon et al., 2012. All replicates (100% of data) were used, in total ~750M reads.
Genome: mapped to hg19 chromosome 14 contigs assembled by Allpaths-LG as part of GAGE
Format: contig_id[tab]bin_start[tab]bin_end[tab]data_i_1[tab]data_i_2[tab]...[tab]data_i_n

contig_positions.tab.gz (contig positions)
Data: Allpaths-LG contigs mapped to hg19 chromosome 14.
Format: contig_id[tab]start_position[tab]end_position

Code is maintained, updated and documented at the DNA Triangulation github repository.

For questions please contact Noam Kaplan.