visualize the whole genome data

[DittmanC]

Hi, I have been trying to use 3D-function "3DMax-3Dmodeler" in the Genomeflow to visualize my hic data. I know that the input file requires a contact matrix in sparse matrix format. I was using hic-straw to extract the matrix file from .hic file. While the hic-straw requires specifying a pair of chromosomes, eg chr1 chr1, chr1 ch2...etc. Inside the matrix file, it contains only 3 columns< genomic location 1>< genomic location 2>. If I generate the matrix file separately and merged them together, still, how can it separate based on the chromosomal level, chr1, chr2, chr3....etc. and If I want to visualize the whole genome data, do you have any idea how could i do that? Many thanks

Best,
Dittman

[OluwadareLab]

Hello DittmanC,

Regarding the 3DMax input, there is a parameter called CHROMOSOME_LENGTH, which allows you to specify the number of points or beads for each chromosome in the input data, separated by commas. These numbers must be consistent with the input data. In the case of merged genome data, the number of points in each chromosome, dependent on the resolution, should correspond to those in the input data. So, yes, you can manually merge data from different chromosomes into one as the genome data. It will just be a continuous row of data from the different chromosome and there's no need to actively separate them. So, after chr1 for example, chr2 will begin, and so on. Since the three-column sparse matrix format uses the first column to signify the chromosome and the second and third columns to represent the start and end positions, with the number of unique starts indicating the number of points in the chromosome.

Regarding the second question about visualization, you just need to follow the input format and provide the Chromosome length parameter for the reconstruction of the genome data.

I hope this clarifies your question.