What is the best and latest package/software for post-processing of Hi-C (Chromosome Conformation Capture)?
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6.1 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 • 1.6k views
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6.1 years ago

HiGlass is useful for visualization with annotations.

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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.

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

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5.6 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

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