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!
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jamespower •
HiGlass is useful for visualization with annotations.
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.
Sorry, that wasn't clear from your question. Hope this was useful, anyway!
What about HiC-pro? https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x
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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