Predicted genome-wide chromatin contact differences among 71 bonobos and chimpanzees
Data files
Nov 01, 2023 version files 744.28 MB
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HFF_comparisons.txt
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README.md
Abstract
This file contains predicted chromatin contact differences in HFF cells using Akita among pairs of 71 bonobos and chimpanzees at 4,420 ~ 1 Mb genomic windows in the panTro6 genome. Each entry corresponds to a pairwise comparison at a given window. Data per comparison includes the individual IDs in the pairwise comparison, lineages represented, chromosome, position, window ID, mean squared error, Spearman correlation, divergence (1 - Spearman correlation), and the number of nucleotide differences for the pair at the given window.
README
This file contains descriptions of the column headers for "HFF_comparisons.txt".
- ind1 = individual 1 in comparison
- ind2 = individual 2 in comparison
- lineages = lineages represented in comparison (ppn = bonobo, pte = Nigeria-Cameroon chimpanzee, pts = eastern chimpanzee, ptt = central chimpanzee, ptv = western chimpanzee)
- chr = chromosome
- window_start = 0-based position in panTro6 coordinates
- window = window ID
- mse = mean squared error between contact maps for individual 1 and individual 2
- spearman = Spearman correlation between contact maps for individual 1 and individual 2
- divergence = 1 - Spearman correlation between contact maps for individual 1 and individual 2
- seq_diff = the number of nucleotide differences between individual 1 and individual 2 for the window
Methods
All data in this file were generated using publicly available datasets (see below). Variants were filtered using bcftools to retain high-quality sites and high-quality genotypes. The dataframe was created using Pandas in a Python Jupyter notebook.
Data used to generate these predictions:
- chimpanzee reference sequence (https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/)
- Illumina short reads for 71 bonobos and chimpanzees (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA189439, https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB15086)