Synteny Studies

[AMAN KUMAR]

Hello 

I am finding it hard to understand the input file formats for syntenic studies. 

Is there any template file available for syntenic studies across genomes?

[Martin Krzywinski]

The format for ribbon between two regions of the genome is a pair of coordinates, followed by an optional list of parameters used in formatting and used by <rules> to control how the ribbon is displayed.

CHR1 START1 END1 CHR2 START2 END2 {PARAMS}

It's up to you to filter and reformat alignments from other software into this format. There are a few utility scripts that I provide to help you do this. See "links" section in 

http://www.circos.ca/documentation/tutorials/configuration/data_files/

m

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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