This is a test version of Biostars. For the public version, visit https://www.biostars.org.
5c Analysis tool

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.

5c
• 3,165 views • link
updated by Ram Ram • written by Prasad Prasad

1 answer

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
• 1 views • link
written by EagleEye EagleEye

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

• 1 views • link
written by Prasad Prasad

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

• 1 views • link
written by EagleEye EagleEye

thanks a lot. i will try this tool

• 1 views • link
written by Prasad Prasad

Log in to answer this question.

More posts like this