Questions tagged [hi-c]

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Can anyone point me towards a HiC Dataset with domains of high confidence?

is there a dataset online containing a HiC contact matrix and file with TAD boundary locations, which were generated, either by hand or automated, with high accuracy? Although I already used programs ...
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2answers
65 views

BWA doesn't recognize HiC options

I'm trying to run bwa on HiC data. This is the command I'm giving: bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq ...
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2answers
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Installing HiC-Pro issues

I am setting up a HiChIPseq pipeline, but installing software necessary for the HiC side of things has been unbecoming. Both my PI and I have tried to install Hi-C Pro onto our Mac Pro that we use as ...
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1answer
22 views

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 ...
1
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1answer
59 views

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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0answers
14 views

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 ...
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1answer
37 views

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 ...
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2answers
1k 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. ...