Home

Welcome to the c-world-encode wiki!

encode/dekkerlab Hi-C HDF5 file format spec:

##hdf.dataset

* interactions - 2d numpy array, matrix container

np.array. shape=(n,n) dtype=float64, compression=gzip, chunks=(blocksize,blocksize)

*chrs

np.array. list of all chromosomes by name

*chr_bin_range

np.array. returns nx2 list. [start,end] index for each chromosome.

*bin_positions

np.array. returns nx3 list. [chrindex,bin_start,bin_end] index for each chromosome.

hdf.attr

*genome

ucsc genome assembly

*restriction_enzyme (next feature release)

*binsize (next feature release)

*numreads (next feature release)

*data_type enzyme (next feature release)