Hi-C analysis and significant interactions

Question

[Bogdan]

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

Answer 1

[komal.rathi]

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

Answer 2

[Ryan Dale]

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.

Answer 3

[Jean-Karim Heriche]

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

Answer 4

[Bogdan]

thank you all for suggestions !

Answer 5

[Ashley Stephen Doane]

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

[Bogdan]

thank you Ashley ! sounds very encouraging !