DOI: 10.5061/dryad.4f4qrfjns
title: Hi-reComb: Constructing recombination maps from bulk gamete Hi-C sequencing

description: Recombination is central to genetics and the evolution of sexually
 reproducing organisms. However, obtaining accurate estimates of
 recombination rates and of how they vary along chromosomes continues to be
 challenging. To advance our ability to estimate recombination rates, we
 present Hi-reComb, a new method and software for the estimation of
 recombination maps from bulk gamete chromosome conformation capture
 sequencing (Hi-C).
description: # Hi-reComb: Constructing recombination maps from bulk gamete Hi-C
 sequencing Dataset DOI: [10.5061/dryad.4f4qrfjns](10.5061/dryad.4f4qrfjns)
 ## Description of the data and file structure The file
 reconstructed_maps.tar.gz contains all the recombination maps generated
 for the above paper in a gzipped tar archive that, after unpacking,
 follows the file structure assumed by the analysis code available
 at [https://github.com/millanek/Hi-reComb_paper_analyses/](https://github.com/millanek/Hi-reComb_paper_analyses/). #### File: reconstructed_maps.tar.gz **Description:** The tar archive contains the following subfolders * maps/simulated: These are the simulated maps underlying Fig. 2 - maps/reconstructed: These are the maps for Fig. 3 * maps/reconstructed/wBootstrap: These are the maps for Fig. 4 - maps/LD: These are the stickleback linkage disequilibrium (LD) -based maps underlying the comparisons in Fig. 5 * maps/reconstructed/wDepth: This file contains the effective depth data underlying Supplementary Fig. 1 ### Variables: Each recombination map (for each chromosome) has three tab-separated columns: 1\) "start coordinate", 2) "end coordinate", and 3) "recombination rate per bp (r)"  The values of "nan" in all the files indicate that the recombination rate could not be determined for a particular region of the chromosome (e.g., because of the 'edge effect' near chromosome ends). In the folder 'maps/LD', the LD-based map for stickleback follows the same format as the other maps, with the exception that a single file contains maps for all the chromosomes, and the first column is the chromosome ID. In the folder 'maps/reconstructed/wBootstrap', the files include the same three columns followed by an additional 50 columns with recombination rate estimates based on bootstrap replicates. In the folder 'maps/reconstructed/wDepth', we provide a file for chromosome 16 of Neolamprologus multifasciatus with information on effective depth, underlying Supplementary Fig. 1. More specifically, the columns are: 'pos' - position on chromosome 16 'ratePerBp' - estimated recombination rate at that position 'EffectiveDepth' - effective depth, plotted in Supplementary Fig. 1 'directReadCoverageConcord' - The number of read pairs bounded by this site indicates the absence of a crossover (X=N) 'directReadCoverageDiscord' - The number of read pairs bounded by this site that indicate crossovers (X=C) ### Sample IDs: T2-2 Neolamprologus multifasciatus H3C2 Astatotilapia calliptera AN01 Astatotilapia nubila H5a2 Aulonocara stuartgranti WB1 Gasterosteus aculeatus (from Walby Lake in Alaska) All file names are identified with these IDs ## Access information For any additional questions, please contact Milan Malinsky at [millanek@gmail.com](mailto:millanek@gmail.com)