Creating Circular genome map

sarbashis · 01-12-2012, 04:08 AM

Could any one suggest me how to create a circular genome map with read coverage track. Thanks in advance.

GenoMax · 01-12-2012, 04:22 AM

See if this will help: http://www.bcgsc.ca/platform/bioinfo/software/circos

sarbashis · 01-12-2012, 09:09 PM

@GenoMax,
Thanks I will check

marcowanger · 01-12-2012, 10:35 PM

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)

maubp · 01-16-2012, 02:16 AM

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.

colindaven · 01-17-2012, 05:41 AM

BRIG looks quite nice, haven't used it yet though

http://sourceforge.net/projects/brig/

jonathanjacobs · 02-28-2012, 10:01 AM

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.

honey · 03-06-2012, 08:11 PM

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

neha · 07-17-2012, 11:49 PM

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

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
How to align SNP coordinates against a circular reference genome?	Lspoor	General	1	02-17-2012 11:44 AM
Creating genome compilation for cis-genome	Martiniano	Bioinformatics	0	07-12-2011 06:39 AM
genome map visualization	NicoBxl	Bioinformatics	1	03-16-2011 08:29 AM
circular genome assembling	mingkunli	Bioinformatics	0	04-06-2010 08:32 AM
from CGH arrays to genome map	fabio25	Bioinformatics	3	09-25-2008 07:08 AM

01-12-2012, 04:08 AM	#1
sarbashis Member Location: India Join Date: Jun 2010 Posts: 17	Creating Circular genome map Could any one suggest me how to create a circular genome map with read coverage track. Thanks in advance.

01-12-2012, 10:35 PM	#4
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	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) __________________ Marco

03-06-2012, 08:11 PM	#8
honey Senior Member Location: Pittsburgh Join Date: Feb 2010 Posts: 151	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

07-17-2012, 11:49 PM	#9
neha Member Location: kolkata Join Date: Oct 2011 Posts: 32	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 10:16 PM.

01-12-2012, 04:22 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	See if this will help: http://www.bcgsc.ca/platform/bioinfo/software/circos

01-12-2012, 09:09 PM	#3
sarbashis Member Location: India Join Date: Jun 2010 Posts: 17	@GenoMax, Thanks I will check

01-16-2012, 02:16 AM	#5
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	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.

01-17-2012, 05:41 AM	#6
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	BRIG looks quite nice, haven't used it yet though http://sourceforge.net/projects/brig/

02-28-2012, 10:01 AM	#7
jonathanjacobs Member Location: Rockville, MD Join Date: Apr 2011 Posts: 23	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.