HiC数据可视化之HiCExplorer

1. 前言

HiC数据可视化工具有R包HiTC（直接支持HiC-pro的输出），HiCPlotter（直接支持HiC-pro的输出）和HiCExplorer（作用矩阵需要使用h5格式，提供工具对.hic文件和hicpro输出的转换），juicerbox（.hic文件），plotgardener（.hic文件），这里先使用hicexplorer对hicpro结果可视化试试看。

2. Try

mamba create -n hicexplorer
mamba activate hicexplorer
mamba install hicexplorer -c bioconda -c conda-forge -y

# 使用hicpro输出
cd /mnt/caigui/41_sk_genome_129M/37_hicpro/Resultes/hic_results/matrix/sample1/iced/20000

hicConvertFormat \
    -m sample1_20000_iced.matrix \
    -o sample1_20000_iced \
    --bedFileHicpro ../../raw/20000/sample1_20000_abs.bed \
    --inputFormat hicpro \
    --outputFormat h5

hicPlotMatrix -m sample1_20000_iced.h5 -o hicPlotMatrix.log1p.png --chromosomeOrder Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 --log1p

vim hic_track.ini

# [x-axis]
# where = top

# [hic matrix]
# file = sample1_20000_iced.h5
# title = Hi-C data
# # depth is the maximum distance plotted in bp. In Hi-C tracks
# # the height of the track is calculated based on the depth such
# # that the matrix does not look deformed
# depth = 300000
# transform = log1p
# file_type = hic_matrix

# [tads]
# file = ../../raw/20000/sample1_20000_abs.bed
# file_type = domains
# border_color = black
# color = none
# # the tads are overlay over the hic-matrix
# # the share-y options sets the y-axis to be shared
# # between the Hi-C matrix and the TADs.
# overlay_previous = share-y

# [spacer]

# [bigwig file test]
# file = Su_H3K27.deeptools.bw
# # height of the track in cm (optional value)
# height = 4
# title = ChIP-seq
# min_value = 0
# max_value = 30

hicPlotTADs --tracks hic_track.ini -o hic_track.png --region Chr3:10000000-14000000

hicConvertFormat \
    -m sample1_20000_iced.matrix \
    -o sample1_20000_iced.cool \
    --bedFileHicpro ../../raw/20000/sample1_20000_abs.bed \
    --inputFormat hicpro \
    --outputFormat cool