Questions tagged [chromosome-capture]

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Get a single number representing the contact probability between a pair of genomic loci using HiC data

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 ...
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How to identify the reference genome assembly used to create a .hic file?

I have a bunch of .hic files of different species. But, I don't know which reference genome assembly (e.g. GRCh37 or GRCh38 in the case of human genome) the genomic co-ordinates of the .hic file ...
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Chromosome information for miRNA

Apologies if this question is previously asked. I have a BAM file alignment to hg19 and miRNA gff3 file from ...
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ChrQ definition

What is ChrQ? I assume it then means chromosme Q or something like that yet when I google for it I get very weird answers, but as I saw that a couple times when looking on freebayes pipelines manuals ...
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Where to assign a read pair when a mate spans a HiC bin boundary?

Chromosome capture experiments, like Hi-C, typically bin the genome into distinct bins. A contact matrix, $M$, is given by $M_{i,j} = |\{pairs | mate_1 \in bin_i, mate_2 \in bin_j\}|$. If one of the ...