How to show ChIA PET data in genome browser?

[Yunjiang Qiu]

I see the GIS ChIA PET track in the browser. Is there a format I can put my own data in genome browser? What I have is a pair of genome loci.

Thanks!

Yunjiang

[Brian Lee]

Dear Yunjiang,

Thank you for using the UCSC Genome Browser and your question about ChIA-PET data.

The best place to start with investigations is at the track description page for this externally ENCODE sourced data, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGisChiaPet

There you will find the methods and the best contact for questions regarding the data, Yijun Ruan. It is best to address your scientific questions about how to interpret and use and recreate the data to Yijun, who is now at the Jackson Laboratory: http://research.jax.org/faculty/yijun-ruan.html

On the Track Description page you will also find some references that could be helpful:
http://www.ncbi.nlm.nih.gov/pubmed/22265404
http://www.ncbi.nlm.nih.gov/pubmed/20069536
http://www.ncbi.nlm.nih.gov/pubmed/19890323
http://www.ncbi.nlm.nih.gov/pubmed/20181287

You may also want to search our mailing list archives when you have questions to see if previous answers may have useful information:
https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/chia-pet

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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