circos for genes with chromosome positions

[remya...@macfast.ac.in]

Dear Sir,

I am using Circos for visualizing some data on genes and markers.

I would like to see the the respective markers on each gene segment. there will be some 37 genes and I need to place them according to their base pair positions like the ideogram segment must be in continuous( if the first segment ends at 350bp, second must start at 351bp) and then I need to mark the snps on their respective bp positions. that would be the outer most layer.

if possible, i need inner circles with same config, but less markers . Hope you understand my image outline.

Remya

[Chris Ulpinnis]

Hi,

I am using Circos to visualize snp data for some selected genes. Do you just want to mark the genes on the ideogram or do you want to "zoom" to the positions on the chromosome on which the genes are located ?

If you just want them to be marked, you can use highlights (I think you can use highlights for the marker positions, too).

Take a look at http://circos.ca/tutorials/lessons/highlights/ideogram_highlights/ .

Regards

Chris

[remya...@macfast.ac.in]

Sir,

I was using circos online..is there an option to include the highlights in circos online.

Thanks for the reply

Remya

[Martin Krzywinski]

The online version provides only a subset of the features and is designed specifically for showing tabular data.

You can toggle the circular bar plots by toggling "hide contribution tracks".

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

--
You received this message because you are subscribed to the Google Groups "Circos" group.
To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.
To post to this group, send email to circos-data-...@googlegroups.com.
Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/d/optout.

[remya...@macfast.ac.in]

Sir,

So If need to make a circle with 25(22+X+Y+ m) chromosomes as segments where I got a bunch of snps... i need to plot the p value at some positions on chromosomes.

how should the table looks like. is there any option to mark the desired points on chromosomes?

Remya

 

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsub...@googlegroups.com.

[remya...@macfast.ac.in]

Hi SIr,

I used Circos plot feature for plotting my P values around 22 chromosomes...

Its not showing any errors when I run it..but its taking so much time even for 25 values..and it was killed when I left it for one overnight...

I just wanted to know ho much time it takes normally for plotting the data..I used the input file in the format

hs1 startpos endpos pvalue

Thanks

Remya 

On Thursday, September 11, 2014 1:22:22 PM UTC+5:30, Martin wrote:

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsub...@googlegroups.com.

[Martin Krzywinski]

How many SNPs are you trying to draw? Please read this document about resolution

http://mkweb.bcgsc.ca/vizbi/2012/resolution/resolution.pdf

The genome is 3Gb and on a 3,000 x 3,000 image you have no more than about 10,000 pixels around the circumference. Drawing more data points than this will result in overplotting -- you won't be able to see any meaningful differences.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.

[remya...@macfast.ac.in]

Dear Sir, 

its 725571 SNPs ..I can upload the conf file and other ideogram files...

How many snps can be included ..the max limit?

Thanks

Remya

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsubsc...@googlegroups.com.

To post to this group, send email to circos-data-...@googlegroups.com.
Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/d/optout.

[Martin Krzywinski]

The limit to the number of SNPs (or any data points) that you can show individually is a combination of the resolution of the figure, limit of visual acuity and our ability to parse complex patterns.

I would suggest that you need to bin the SNPs into <5,000 windows.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.