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Old 01-18-2011, 08:33 AM   #1
Lspoor
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Location: Fife, Scotland

Join Date: Mar 2010
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Question How to align SNP coordinates against a circular reference genome?

I have a list (tab-delimited file) of approximately 18 000 SNP coordinates for a bacterial reference genome GenBank file (When compared to one other query FASTA genome sequence using "dnadiff" function of Mummer3).

I am looking to produce a circular representation of this reference genome, with the SNP coordinates mapped against it, to look for hotspots that might indicate recombination events may have occurred. I basically want to look at the SNP distribution throughout the genome.

For smaller numbers of SNPS (1000 to 2000), I was using an open source software called BRIG but am unable to get this to work with the much larger SNP numbers?

Does anyone have any suggestions for another (vaguely user-friendly way!) I could do this, as am a relative Newbie to Linux but also have access to Windows. I have produced an OK-ish diamgram using GenomeDiagram with Biopython but it is not easy to maniupulate the diagram to get a better look at the SNP distribution )eg change the size or width of the features representing the SNPS).

Any suggestions would be very much appreciated!
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Old 02-17-2012, 11:44 AM   #2
houkto
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Hi there,

I am trying to achieve the same thing. I believe almost everyone is going for http://circos.ca/ you can install it in windows or linux and it very well documented and they have a forum in which you can troubleshoot your problems. if you find something else please let me know.

Cheers
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