Question

What is the best and latest package/software for post-processing of Hi-C (Chromosome Conformation Capture)?

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6.6 years ago

jamespower ▴ 100

I am new to Hi-C data analyses and I am looking for the latest package and references on how to overlap this type of data with GWAS and genes. Thanks for suggestions!

Hic R gwas next-gen gene • 1.8k views

ADD COMMENT • link updated 6.1 years ago by afli ▴ 190 • written 6.6 years ago by jamespower ▴ 100

score 3 · Answer 1 · 2018-04-21

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6.6 years ago

Alex Reynolds 36k

HiGlass is useful for visualization with annotations.

ADD COMMENT • link 6.6 years ago by Alex Reynolds 36k

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Thank you, I think HiGlass is mostly to view the data, while I was wondering about the pipeline/packages used for calling an interaction significant and overlapping with GWAS SNPs.

ADD REPLY • link 6.6 years ago by jamespower ▴ 100

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Sorry, that wasn't clear from your question. Hope this was useful, anyway!

ADD REPLY • link 6.6 years ago by Alex Reynolds 36k

score 3 · Answer 2 · 2018-11-03

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6.1 years ago

afli ▴ 190

What about HiC-pro? https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x

ADD COMMENT • link 6.1 years ago by afli ▴ 190

score 1 · Answer 3 · 2018-11-02

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6.1 years ago

mario.looso ▴ 30

You might use the UROPA annotation package, it is able to annotate BED files with whatever GTF files (your SNPs) simply by generating a configuration file that allows to fine tune the annotation: https://www.nature.com/articles/s41598-017-02464-y

ADD COMMENT • link 6.1 years ago by mario.looso ▴ 30