Tweet
Could any one suggest me how to create a circular genome map with read coverage track. Thanks in advance.
-
-
See if this will help: http://www.bcgsc.ca/platform/bioinfo/software/circos -
@GenoMax,
Thanks I will checkComment
-
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)MarcoComment
-
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.Comment
-
BRIG looks quite nice, haven't used it yet though
Comment
-
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.Comment
-
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.
ThanksComment
-
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,
NehaLast edited by neha; 07-19-2012, 09:16 PM.Comment
-
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.Yesterday, 11:43 AM
-
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before... -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
Comment