Looking For Information On Hi-C (Chromosome Conformation Capture) Analysis: Workflows, Best Practices

Question

[cheater149]

I am new to Hi-C analysis.I am working with a test data set.can any one give me a clear work flow of Hi-C analysis and also can any one tell me about the maths behind the expected matrix and inter and intra chromosomal maps

Answer 1

[Ben]

You're essentially asking "can someone tell me everything I need to do and why", while also not saying what you are aiming to do with this data.

Have you read the key papers? Yaffe and Tanay (2011), Lieberman Aiden et al. (2009), Dixon et al. (2012)? The supplementary of Dixon et al. is quite detailed. There's also a decent quick tutorial hosted at BioConductor (pdf, R) that walks you through extracting PC eigenvectors from Lieberman's intrachromosomal data and getting some matching chromatin features.

Answer 2

[14134125465346445]

HOMER contains a HI-C analysis tutorial:
http://biowhat.ucsd.edu/homer/interactions/index.html
http://biowhat.ucsd.edu/homer/interactions/HiCtips.html

A quote:

Hi-C is a beast of an assay. There is a lot of information in each run, and the size and complexity of the experiments can stretch the limits of your computer too.

[Mikael Huss]

Seconded, I think this is the tool closest to a "standard workflow" at the moment

[Raghav]

homer is quit good for HiC analysis but when I am trying follow it for HiC data I stuck at the first step and unable to makeTagDirectory. makeTagDirectory HiC-Unprocessed reads1-1.sam,reads1-2.sam reads2-1.sam,reads2-2.sam -tbp 1

because I have paired end illumina sequence and when I mapped it with bowtie2 i have given 2 fastq files r1 and r2 and got single output sam file, I don't be able to use out put sam file for further downstream analysis through HOMER

[cheater149]

using samtools convert it to bam n go ahead with homer analysis

Answer 3

[Anton Goloborodko]

I would recommend a recent review of Hi-C data analysis by Job's Dekker lab. It gives a nice overview of the features of Hi-C data and the method itself, which is arguably more important right now than particular mathematical models of these features.

Answer 4

[PoGibas]

If you want Hi-C mathematics I suggest to look at the recent Nucleic Acids Research paper: A complex network framework for unbiased statistical analyses of DNA–DNA contact maps.

...Here we present a general statistical framework that is widely applicable to the analysis of genomic contact maps...we present a robust method for generating randomized contact networks...