5c Analysis tool

Question

[Prasad]

hi,

I am very new to chromosome conformation capture data and have received multiple samples 5C data. I had gone through HiFive (couldn't understand the fragment input) and HiTC package. Gone through the thread Hic, most of the tools are for Hic data. Is there a pipeline or tool for analysis from fastq to interaction point identification with some good visualization.

Any suggestions are appreciated.

Answer 1

[EagleEye]

After alignment follow this pipeline.

http://homer.salk.edu/homer/interactions/

This requires following tools to be installed on your system,

3rd Party Software

• Java tree view
• circos
• R
• Cytoscape

[Prasad]

thanks for the reply. This is for HiC, would it work for 5C data as well because i have the data for 5C method

[EagleEye]

In my opinion the tools used for HiC data can handle 5C too. Please also refer following articles and see if you can get some idea about the analysis.

Examples:

http://www.nature.com/nrg/journal/v14/n6/fig_tab/nrg3454_F1.html

5C articles:

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

http://www.nature.com/nsmb/journal/v18/n1/full/nsmb.1936.html

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581439/

A complex network framework for unbiased statistical analyses of DNA–DNA contact maps

http://nar.oxfordjournals.org/content/41/2/701.full.html?etoc

[EagleEye]

Did you try HiCUP ?

http://www.bioinformatics.babraham.ac.uk/projects/hicup/

[Prasad]

thanks a lot. i will try this tool