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Old 01-12-2012, 03:08 AM   #1
sarbashis
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Default Creating Circular genome map

Could any one suggest me how to create a circular genome map with read coverage track. Thanks in advance.
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Old 01-12-2012, 03:22 AM   #2
GenoMax
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See if this will help: http://www.bcgsc.ca/platform/bioinfo/software/circos
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Old 01-12-2012, 08:09 PM   #3
sarbashis
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@GenoMax,
Thanks I will check
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Old 01-12-2012, 09:35 PM   #4
marcowanger
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Circos is probably the most commonly used one.

Others include

CGview (http://wishart.biology.ualberta.ca/cgview/)
DNAPlotter (http://bioinformatics.oxfordjournals.../25/1/119.full)
GenomeViz (http://www.biomedcentral.com/1471-2105/5/198)
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Old 01-16-2012, 01:16 AM   #5
maubp
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You can also use GenomeDiagram in Biopython to draw a circular genome with a coverage depth plot round it - but this is a programmatic interface.
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Old 01-17-2012, 04:41 AM   #6
colindaven
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BRIG looks quite nice, haven't used it yet though

http://sourceforge.net/projects/brig/
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Old 02-28-2012, 09:01 AM   #7
jonathanjacobs
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BUMPED.

Thank you for this. We're using CLC Bio for routine analysis (which is really nice) but it doesn't support circular genome maps at the moment.

So far BRIG has done what I need. CIRCOS looks gorgeous, after 2 hours installing and configuring all the perl libraries needed to support it, I caved and gave up. Maybe I try again in a week or so.
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Old 03-06-2012, 07:11 PM   #8
honey
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Default circos

I have to plot a seq uencing data in circle and wonder what tool wil be used. I found Circos but is not window based and intutive for a biologist. Is there a version of CIRCOS which can be easily used or any alternative tool. It is a human genome based data.

Thanks
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Old 07-17-2012, 10:49 PM   #9
neha
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Default Regarding DNAplotter

Hello everyone

I have done re-sequencing of one of Vibrio cholerae strain and has data in form of consensus sequence for both the chromosomes. Now I want to make these consensus circular and compare them with the reference . Is it possible to do that with DNAplotter? I mean I want that outer circle should be my reference sequence and the inner circle should me my consensus sequence.

I am trying to use DNAplotter but not getting much. please pardon me if I am missing something very obvious.

Regards,
Neha

Last edited by neha; 07-19-2012 at 09:16 PM.
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