Best Software for analysis of Hi-C data

Question

[h.long]

Hi,

I am just getting started analyzing Hi-C data to call TADs. It seems that there is not yet a consensus on which software tools are best to make an analysis pipeline. I have so far tried Hicup (from Babraham) for alignments, homer for making heatmaps and have been trying to install Juicer which offers a full pipeline.

I am wondering if anyone has any advice on which software tools they use in their analysis workflow. I would be particularly interested advice as to which is the best TAD caller to use.

Thanks for your help!

Answer 1

[Devon Ryan]

I'll give the somewhat biased recommendation to try HiCExplorer. It will enable starting with fastq files and proceeding through heatmaps and further analysis.

[h.long]

Hi Devon,

Thanks for your suggestion. The original publication for HiCExplorer was done on drosophila but I assume it can also be used for high organisms such as humans and mice?

Thanks!

[Devon Ryan]

Sure, mammalian genomes work just fine. We like to use fruit fly for development because their genomes are small, so it's (A) much cheaper to sequence and (B) much quicker to process. But we commonly use mouse and human samples with HiCExplorer these days.

Answer 2

[steve]

I have not used it but I just wanted to point out that there's a Hi-C pipeline in nf-core;

https://nf-co.re/hic/usage

https://github.com/nf-core/hic