Hello to the experts in analyzing chromosome structure data in HiC format,
I have a very basic question. I have a HiC file (specifics are mentioned below), using which I would like to obtain contact probability between a pair of genomic loci. I obtained contact probabilities between the two loci at different resolutions available in the HiC file. However, rather than having a vector of contact probabilities, I would like to have a single number that appropriately represents the contact probability between the loci.
My guess is that there could be two ways to get a single number as the contact probability between two given genomic loci.
- Should I take the highest contact probability? or,
- Depending on the lengths of the genomics loci of interest, may be the resolution that is close to that could be selected as a single number that represents the contact probability between the loci. Eg. with this strategy, if genomic loci of interest are ~5kb in length the contact probability at 5kb resolution is selected as a single number. Then, the issue is that the length of the genomic loci of interest could be lower than the lowest length of resolution available in the HiC file.
- Contact probabilities at different resolutions could be aggregated. Then I wonder what would be the appropriate way to aggregate contact probabilities, e.g. by multiplication or median or something else.
Just to reiterate, above these are my guess and I am not sure whats the best way. So basically my question is: how can I get a single number that would represent the contact probability between a pair of genomic loci using HiC data?
Some specifics that might be useful in answering my question.
- source of the HiC file: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_K562_combined_30.hic
- organism: human (K562 cell line)
- Resolutions in HiC data (bp): [2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000]
- Type of genomic loci: upstream non-coding regions of the genes
- lengths of genomic loci of interest: average ~1000bp (range: 500-5000bp).
- software I am using to "extract" data from HiC file: https://github.com/aidenlab/straw