Raw Contact Maps

In this step HiCPack will generate binned matrix files via C++ Executable file build_matrix.

Additional quality controls such as fragment size distribution can be extracted from the list of valid interaction products. We usually expect to see a distribution centered around 300 pb which correspond to the paired-end insert size commonly used. The fraction of duplicates is also presented. A high level of duplication indicates a poor molecular complexity and a potential PCR bias. Finally, an important metric is to look at the fraction of intra and inter-chromosomal interactions, as well as long range (>20kb) versus short range (<20kb) intra-chromosomal interactions.

The contact maps are then available in the hic_results/matrix folder. Raw contact maps are in the raw folder. Note that Normalization methods are not supported in HiCPack. The contact maps are generated for all specified resolution (available in HiCPack config file) A contact map is defined by:

• BED File: A list of genomic intervals related to the specified resolution (BED format). Here's a sample of a BED file:

chr1    0   20000   1
chr1    20000   40000   2
chr1    40000   60000   3
chr1    60000   80000   4
chr1    80000   100000  5
chr1    100000  120000  6
chr1    120000  140000  7

• Matrix of Interactions File: A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix. The user can specified if the 'upper', 'lower' or 'complete' matrix has to be stored.

Here's a sample of an interaction matrix file:

1   34467   10
3   501 2
3   72  19
3   7516    11
...