Computes differential TADs by comparing the precomputed TAD regions of the target matrix with the same regions of the control matrix. Please notice that the matrices need to have the same read coverage, this can be achieved with hicNormalize and the ‘smallest’-mode. H0 is the assumption that two regions are identical, the rejected files contain therefore the as differential considered regions.

usage: hicDifferentialTAD [--targetMatrix TARGETMATRIX]
[--controlMatrix CONTROLMATRIX]
[--outFileNamePrefix OUTFILENAMEPREFIX]
[--pValue PVALUE]
[--help] [--version]


## Required arguments¶

--targetMatrix, -tm

The matrix which was used to compute the TADs

--controlMatrix, -cm

The control matrix to test the TADs for a differential interaction pattern.

--outFileNamePrefix, -o

Outfile name prefix to store the accepted / rejected H0 TADs.

## Optional arguments¶

--pValue, -p

H0 is considered as ‘two regions are identical.’ i.e. all regions with a test result of <= p-value are rejected and considered as differential.

Default: 0.05

--mode, -m

Default: “all”

--modeReject, -mr

Possible choices: all, one

All test of a mode must be rejected (all) or reject region (and accept it is differential) as soon as at least one region is having a p-value <= –pValue.

Default: “one”

Number of threads to use, the parallelization is implemented per chromosome.

Default: 4

--version

show program’s version number and exit

hicDifferentialTAD computes with a treatment Hi-C file, a control Hi-C file and a precomputed TAD domains file if the detected TADs are differential between the treatment and the control sample. The TADs need to be precomputed on the treatment file with _hicFindTADs.

## Example usage¶

\$ hicDifferentialTAD -tm GSM2644945_Untreated-R1.100000_chr1.cool -cm GSM2644947_Auxin2days-R1.100000_chr1.cool -td untreated_R1_domains.bed -o differential -p 0.01 -t 4 -mr all


In this example data from Nora et al. “Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization”, Cell 169.5 (2017): 930-944 is used [GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98671]

The output are two BED-similar files: the ‘_accepted.diff_tad’ and ‘_rejected.diff_tad’ file. The difference to a real BED file is a) the usage of a header starting with ‘#’, the first six columns are BED6 standard, however, there are three additional columns with the p-values of each intra-TAD, left-inter-TAD and right-inter-TAD test. The score value and name is copied from the domains.bed file which is a output of hicFindTADs.

# Created with HiCExplorer's hicDifferentialTAD version 3.5-dev
# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.
# Rejected regions with Wilcoxon rank-sum test to p-value: 0.01  with used mode: all and modeReject: all