GenArch software for whole genome 3D reconstruction
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GenArch.m
README.md
centromere.m

README.md

GenArch

GenArch is pipeline written in Matlab able to compute whole genome high resolution 3D structure.

Description

It has been conceived and developed to overcome common computational limitations typical of 3D modeling, especially in the context of single-cell Hi-C, enabling the calculation of the 3D architecture of an individual genome at a usually unattainable resolution.

Table of Contents

  • Prerequisites
  • Download
  • Usage
    1. Initial parameters
    2. Load necessary data
    3. Run the script
  • Licence
  • Citation

Prerequisites

GenArch is a Matlab script. Therefore it requires Matlab software.

It assumes that the users has:

  • Hi-C contact matrixes in the full format, at different resolutions
    • the whole genome Hi-C map at low resolution
    • the intra-chromosomal Hi-C maps at medium resolution
    • the intra-chromosomal Hi-C maps at the resolution used to identify TAD boundaries (called TADsRes)
    • the Hi-C matrixes (diagonal blocks) corresponding to TADs at high resolution
  • computed 3D structures (with any desired 3D reconstruction algorithm) in the Nx3 matrix format, where N is equal to the number of points of the structure, i.e. to the number of bins in the corresponding matrix, and the three columns correspond to the 3D coordinates x, y, z
    • the low resolution whole-genome 3D structure
    • the medium resolution chromosomal 3D structures
    • the high resolution TADs 3D structures
  • array containing the length of each chromosome in the low resolution Hi-C map (i.e. number of bins)
  • array of TAD boundaries position (i.e. bins of the TADs-resolution matrix in which there is a TAD boundary), one for each chromosome

Download

The script GenArch.m can easily be download from this repository.

Usage

  1. Open the script and modify the initial parameters in the first section with the values adapted for your study.
  2. Load in Matlab the necessary data.
  3. Finally, run the script.
    • Main output
    • Additional outputs

1. Initial parameters

In the first section there are 5 initial parameters to modify: C, LowRes, TADsRes, MedRes and HiRes. Note that resolution values are expressed in bp, therefore 100000 indicates 100 kb.

When opening GenArch for the first time, you will see the following:

% this section must be modified with the values adapted for the user's
% study case

C = 20; % chromosomes number
LowRes = 10000000; % enter the chosen low resolution (to compute whole-genome reference structure)
TADsRes = 2000000; % enter the chosen TADs-resolution (to identify TAD boundaries)
MedRes = 1000000; % enter the chosen medium resolution (to compute chromosomes structure)
HiRes = 100000; % enter the chosen high resolution (to compute TADs structure)

ResRatioT = TADsRes/HiRes; % scaling factor between the resolution used to identify TAD boundaries and the high resolution (used to compute TADs structure)
ResRatioM = MedRes/HiRes; % scaling factor between the medium resolution (used to compute chromosomes structure) and the high resolution (used to compute TADs structure)
  • C is the number of chromosomes in the studied genome. Replace 20 with the actual number of chromosomes.
  • LowRes is the resolution at the whole-genome level. It is the same resolution of the whole-genome Hi-C matrix (named M_LowRes in the script) and of the low resolution whole-genome 3D structure (called XYZ_LowRes_gen). Replace 10000000 with the actual chosen low resolution.
  • TADsRes is the resolution used to identify TAD boundaries. It is the same resolution of the intra-chromosomal Hi-C matrixes (named M_TADsRes_#c in the script). Replace 2000000 with the actual chosen resolution.
  • MedRes is the resolution at the chromosomal level. It is the same resolution of the chromosomal Hi-C matrixes (named M_MedRes_#c in the script) and of the medium resolution chromosomal 3D structures (called XYZ_MedRes_chr#c). Replace 1000000 with the actual chosen medium resolution.
  • HiRes is the resolution at the TADs level. It is the same resolution of the TADs Hi-C matrixes (named M_HiRes_#c in the script) and of the high resolution TADs 3D structures (called XYZ_HiRes_chr#c_TAD#t). Replace 100000 with the actual chosen high resolution.

2. Load necessary data

The user must load the following data:

  • M_LowRes: whole-genome low resolution (set at LowRes initial parameter) Hi-C matrix, comprehensive of intra- and inter-chromosomal data, with chromosomes ordered with ascending order numbers.
  • XYZ_LowRes_gen: low resolution (set at LowRes initial parameter) 3D structure of the whole genome, computed with the favorite 3D reconstruction algorithm, in the Nx3 matrix format (with N equal to the number of points of the structure, i.e. to the number of bins in M_LowRes matrix, and the three columns corresponding to the 3D coordinates x, y, z).
  • L_LowRes: array of C (i.e. number of chromosomes) components, where each coefficient is equal to the number of bins (length) of each chromosome in the low resolution contact map M_LowRes.
  • M_TADsRes_#c: intra-chromosomal contact map of each chromosome at the resolution used to compute TAD boundaries (set at TADsRes initial parameter). The symbols #c must be replaced with the actual chromosome number (for example, replace #c with 1 for chromosome 1, so that M_TADsRes_#c becomes M_TADsRes_1). A total of C matrixes must be uploaded.
  • TB_TADsRes_#c: array of TAD boundaries position, one for each chromosome. Each array is as long as the number of TAD boundaries identified in the corrisponding chromosome and its coefficients are equal to the number of the bins of the matrix M_TADsRes_#c identified as boundaries. The symbols #c must be replaced with the actual chromosome number (for example, replace #c with 1 for chromosome 1, so that TB_TADsRes_#c becomes TB_TADsRes_1). A total of C arrays must be uploaded.
  • M_MedRes_#c: intra-chromosomal contact map of each chromosome at medium resolution (set at MedRes initial parameter). The symbols #c must be replaced with the actual chromosome number (for example, replace #c with 1 for chromosome 1, so that M_MedRes_#c becomes M_MedRes_1). A total of C matrixes must be uploaded.
  • XYZ_MedRes_chr#c: medium resolution (set at the MedRes initial parameter) 3D structure of each chromosome, computed with the favorite 3D reconstruction algorithm from MedRes intra-chromosomal contact maps (here called S.MedRes.mapp_regs.chr_#c, with the symbols #c replaced by the actual chromosome number -- S.MedRes.mapp_regs.chr_1 for chromosome 1) which result from the removal of the centromeric region. The 3D structure is in the Nx3 matrix format (with N equal to the number of points of the structure, i.e. to the number of bins in S.MedRes.mapp_regs.chr_#c matrix, and the three columns corresponding to the 3D coordinates x, y, z). The symbols #c must be replaced with the actual chromosome number (for example, replace #c with 1 for chromosome 1, so that XYZ_MedRes_chr#c becomes XYZ_MedRes_chr1). A total of C structures must be uploaded.
  • M_HiRes_#c: intra-chromosomal contact map of each chromosome at high resolution (set at HiRes initial parameter). The symbols #c must be replaced with the actual chromosome number (for example, replace #c with 1 for chromosome 1, so that M_HiRes_#c becomes M_HiRes_1). A total of C matrixes must be uploaded.
  • XYZ_HiRes_chr#c_TAD#t: high resolution (set at HiRes initial parameter) 3D structure of each TAD, computed with the favorite 3D reconstruction algorithm from HiRes matrix diagonal blocks (here called S.HiRes.mapp_regs.chr_#c.block_#t, with the symbols #c replaced by the actual chromosome number and the symbols #t replaced by the TAD number -- S.HiRes.mapp_regs.chr_1.block_1 for the first TAD of chromosome 1) corresponding to TADs which result from the removal of the centromeric region. The 3D structure is in the Nx3 matrix format (with N equal to the number of points of the structure, i.e. to the number of bins in S.HiRes.mapp_regs.chr_#c.block_#t matrix, and the three columns corresponding to the 3D coordinates x, y, z). The symbols #c must be replaced with the actual chromosome number and the symbols #t by the TAD number (for example, replace #c with 1 and #t with 1 for TAD 1 of chromosome 1, so that XYZ_HiRes_chr#c_TAD#t becomes XYZ_HiRes_chr1_TAD1). A total of C x T(i) (with T(i) equal to the number TADs of chromosome i) structures must be uploaded.

3. Run the script

Once having saved the script with the parameters modified as indicated in paragraph 1 and having loaded in Matlab all the necessary data listed in paragraph 2, just run it.

Main output

The pipeline creates a Matlab structure (S) and the final output, obtained with the multi-scale (3-levels) optimal alignment procedure, is stored in two ways:

  • S.LowRes.XYZ_Hi_aligned: high resolution 3D structures of individual chromosomes
  • S.LowRes.XYZ_GENOME: high resolution 3D structure of the whole genome, not separating chromosomes.

Additional outputs

The first level of the structure S contains 4 fields: LowRes, TADsRes, MedRes and HiRes.

1. Fields in LowRes
  • Map: whole-genome low resolution Hi-C matrix (M_LowRes)
  • XYZ_gen: low resolution 3D structure of the whole genome (XYZ_LowRes_gen)
  • length_chrs: length of each chromosome (i.e. number of bins of each chromosome in the low resolution Hi-C map)
  • XYZ_chrs: low resolution 3D structures of each chromosome
  • XYZ_Med_aligned: medium resolution 3D structures of each chromosomes, resulted from the optimal alignment of the medium resolution chromosomal 3D structures (S.MedRes.XYZ_mapp_regs) on the low resolution chromosomal 3D structures (S.LowRes.XYZ_chrs)
  • XYZ_Med_aligned: medium resolution 3D structures of each chromosome, resulted from the optimal alignment of the medium resolution chromosomal 3D structures (S.MedRes.XYZ_mapp_regs, discarding unmappable centromeric regions) on the low resolution chromosomal 3D structures (S.LowRes.XYZ_chrs)
  • XYZ_Hi_aligned: high resolution 3D structures of each chromosome, resulted from the application to the high resolution chromosomal 3D structures (stored in S as S.MedRes.XYZ_Hi_chrs -- see below -- discarding unmappable centromeric regions, already aligned to the medium resolution chromosomal 3D structures) of the optimal alignment transform calculated between the medium resolution chromosomal 3D structures (S.MedRes.XYZ_mapp_regs, discarding unmappable centromeric regions) and the low resolution chromosomal 3D structures (S.LowRes.XYZ_chrs)
  • XYZ_GENOME: high resolution 3D structure of the whole genome, resulted from the concatenation of high resolution 3D structures of each chromosome, optimally aligned in the genome (XYZ_Hi_aligned)
2. Fields in TADsRes
  • Maps_chrs: intra-chromosomal Hi-C matrixes at the resolution set in TADsRes as initial parameter
  • TB_chrs: array of TAD boundaries position (i.e. bin of the TADs-resolution matrix in which there is a TAD boundary)
3. Fields in MedRes
  • Maps_chrs: medium resolution intra-chromosomal Hi-C matrixes (M_MedRes_#c)
  • length_chrs: length of each chromosome (i.e. number of bins of each chromosome in the medium resolution Hi-C map)
  • idx_chrs: logical array for each chromosome with 1 in bins corresponding to the centromeric region (i.e. null bins in the medium resolution intra-chromosomal contact map S.MedRes.Maps_chrs)
  • mapp_regs: medium resolution intra-chromosomal Hi-C maps after the removal of the centromeric region from S.MedRes.Maps_chrs)
  • XYZ_mapp_regs: medium resolution 3D structures of each chromosome computed from S.MedRes.mapp_regs (only mappable regions)
  • XYZ_chrs: medium resolution 3D structures of each chromosome, re-introducing all bins (assigning null coordinates to unmappable centromeric regions)
  • TADs_dim: TADs dimensions (i.e. number of bins of the corresponding medium resolution matrix block)
  • TADs_start: starting bin of each TAD in each intra-chromosomal medium resolution matrix S.MedRes.Maps_chrs (including unmappable centromeric regions)
  • TADs_end: ending bin of each TAD in each intra-chromosomal medium resolution matrix S.MedRes.Maps_chrs (including unmappable centromeric regions)
  • XYZ_TADs: medium resolution 3D structures of each TAD in each chromosome (including unmappable centromeric regions)
  • XYZ_TADs_mapp: medium resolution 3D structures of each TAD in each chromosome (discarding unmappable centromeric regions)
  • XYZ_Hi_aligned: high resolution 3D structures of each TAD, resulted from the optimal alignment of the high resolution TADs 3D structures (S.HiRes.XYZ_mapp_regs, discarding unmappable centromeric regions) on the medium resolution TADs 3D structures (S.MedRes.XYZ_TADs_mapp, discarding unmappable centromeric regions)
  • XYZ_Hi_chrs: high resolution 3D structures of each chromosome, resulted from the concatenation of TADs high resolution 3D structures S.MedRes.XYZ_Hi_aligned for each chromosome (discarding unmappable centromeric regions)
4. Fields in HiRes
  • Maps_chrs: high resolution intra-chromosomal Hi-C matrixes (M_HiRes_#c)
  • TB_chrs: array of TAD boundaries position (i.e. bin of the high resolution matrix S.HiRes.Maps_chrs in which there is a TAD boundary)
  • blocks_chrs: high resolution Hi-C contact maps of each TAD in each chromosome, corresponding to diagonal blocks in the high resolution intra-chromosomal Hi-C maps S.HiRes.Maps_chrs (including unmappable centromeric regions)
  • TADs_dim: TADs dimensions (i.e. number of bins of the corresponding matrix blocks S.HiRes.blocks_chrs)
  • TADs_start: starting bin of each TAD in each intra-chromosomal high resolution matrix S.HiRes.Maps_chrs (including unmappable centromeric regions)
  • TADs_end: ending bin of each TAD in each intra-chromosomal high resolution matrix S.HiRes.Maps_chrs (including unmappable centromeric regions)
  • idx_blocks_chrs: logical array for each TAD-block with 1 in bins corresponding to the centromeric region (i.e. null bins in the high resolution TAD-block S.HiRes.blocks_chrs)
  • mapp_regs: high resolution Hi-C maps of each TAD in each chromosome, after the removal of the centromeric region from S.HiRes.blocks_chrs
  • XYZ_mapp_regs: high resolution 3D structures of each TAD in each chromosome (discarding unmappable centromeric regions)
  • XYZ_TADs_chrs: high resolution 3D structures of each TAD in each chromosome (including unmappable centromeric regions)
  • num_TADs_chrs: number of TADs in each chromosome

Author

License

Citation

Acknowledgments