hicInterIntraTAD

Extracts and computes different inter and intra TAD values and ratios.

usage: hicInterIntraTAD [--matrix MATRIX] [--tadDomains TADDOMAINS]
                        [--outFileName OUTFILENAME]
                        [--outFileNameRatioPlot OUTFILENAMERATIOPLOT]
                        [--fontsize FONTSIZE] [--dpi DPI] [--threads THREADS]
                        [--help] [--version]

Required arguments

--matrix, -m

The matrix which was used to compute the TADs

--tadDomains, -td

The TADs domain file computed by hicFindTADs.

--outFileName, -o

Outfile name

Default: “output_interintra_tad.tzt”

Optional arguments

--outFileNameRatioPlot, -op

Outfile name for the inter-left/intra vs inter-right/intra ratio plot

Default: “ratio.png”

--fontsize

Fontsize in the plot for x and y axis.

Default: 15

--dpi

The dpi of the scatter plot.

Default: 300

--threads, -t

Number of threads to use, the parallelization is implemented per chromosome (Default: 4).

Default: 4

--version

show program’s version number and exit

This tool computes and extracts for given TADs the inter-left, inter-right and intra-TAD data: the absolute number of contacts, the density (non-zero contacts / all possible contacts) and the ratio of inter-left/intra, inter-right/intra and (inter-left + inter-right)/intra TAD contacts. The data is saved in one file where it can be used for further, user-specific computations outside of HiCExplorer. Also a scatter plot of the ratio inter-left/intra vs. inter-right/intra is created.

# Created with HiCExplorer's hicInterIntraTAD version 3.7-dev
# Chromosome        start   end     name    score   strand  inter_left_sum  inter_right_sum inter_left_density      inter_right_density     inter_left_number_of_contacts   inter_right_number_of_contacts  inter_left_number_of_contacts_nnz       inter_right_number_of_contacts_nnz      intra_sum       intra_number_of_contacts        intra_number_of_contacts_nnz    intra_density   inter_left_intra_ratio  inter_right_intra_ratio inter_left_inter_right_intra_ratio
chr1        4400000 6200000 ID_0.01_1       -0.5630275      .       0       265.6981737879304       0       1.0     0       180     0       180     780.0186987409819       324     324     1.0     0.0     0.340630518494993       0.340630518494993
chr1        6200000 7300000 ID_0.01_2       -0.235798       .       288.00513572726237      327.503479611623        1.0     1.0     198     231     198     231     339.91508704783513      121     121     1.0     0.8472855330682405      0.9634861531331044      1.8107716862013452
chr1        7300000 9500000 ID_0.01_3       -0.44334        .       340.12385944568155      159.40880484157745      1.0     1.0     242     110     242     110     1078.1133262629996      484     484     1.0     0.31548061892958207     0.14785904316211984     0.46333966209170185
chr1        9500000 10100000        ID_0.01_4       -1.021538       .       186.65816676710497      124.2235190772146       1.0     1.0     132     84      132     84      118.58286349492002      36      36      1.0     1.5740737005823884      1.0475672067282826      2.6216409073106712
../../_images/ratio.png