Question: 5c Analysis tool
0
gravatar for Prasad
4.4 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

hi,

I am very new to chromosome conformation capture data and have received multiple samples 5C data. I had gone through HiFive (couldnt 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.

tool 5c • 1.6k views
ADD COMMENTlink modified 4.4 years ago by EagleEye6.7k • written 4.4 years ago by Prasad1.6k
0
gravatar for EagleEye
4.4 years ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:

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
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by EagleEye6.7k

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

ADD REPLYlink written 4.4 years ago by Prasad1.6k
1

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

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by EagleEye6.7k

Did you try HiCUP ?

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

ADD REPLYlink written 4.4 years ago by EagleEye6.7k

thanks a lot. i will try this tool

ADD REPLYlink written 4.4 years ago by Prasad1.6k
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