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Questions tagged [hi-c]

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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 ...
0
votes
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Python module bamtags

Does anyone know this python module, bamtags? I'm using a pipeline (Dovetail Genomics, HiRise) that imports it, but it seems it doesn't exist. It's impossible to install it and there is no ...
5
votes
2answers
317 views

What is the correct way to map Hi-C data with bwa mem?

Library Prep I have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. ...