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Hi-C analysis and significant interactions

Dear all,

any recommendation please regarding a Hi-C analysis package that not only implements a set of normalization techniques, but also calls the significant interactions ? thanks !

-- bogdan

next-gen
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updated by Ashley Stephen Doane • Ashley Stephen Doane • written by Bogdan Bogdan

5 answers

You can use HiCUP to map HiC data (SAM/BAM output) followed by the Bioc package GOTHiC or Seqmonk to get significant interactions.

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written by komal.rathi komal.rathi

HiFive (paper, code, docs) implements several normalization strategies so you can try multiple ones using the same framework. See the conclusions section of the paper for normalization algorithm recommendations. However there's no calling of significant interactions that I'm aware of.

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written by Ryan Dale Ryan Dale

There's a pretty comprehensive list on omictools.com.

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written by Jean-Karim Heriche Jean-Karim Heriche

thank you all for suggestions !

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written by Bogdan Bogdan

HiC-Pro has worked well for me for processing and normalisation, and was fairly easy to run parallel array jobs on an SGE compute cluster with it's built scripts. You can then use the bioconductor package HiTC by the same author, or any other options that take a contact matrix. cheers Ashley

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written by Ashley Stephen Doane • Ashley Stephen Doane

thank you Ashley ! sounds very encouraging !

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written by Bogdan Bogdan

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