how to generate circos image of snp and indel across chromosomes

[ajay kumar]

Dear All,

i am newbie and try to generate circos image of snp and indels across 12 chromosomes i have successfully generated the image which shows the distribution of snp across 12 chromosome in one ring which colored blue, now i want to show the indel (indel.txt -included in zip file) which belongs to the same organism in same circle but in the different ring with different color but could not able to generate that image i am stuck at this point from past one week. for your reference please see the attached generated image and also my complete circos folder.



your kind help is highly appreciated


Thanks

Ajay K Mahato

[Martin Krzywinski]

You're almost there. Just add another <plot> block, associate it with the indel.txt file and change the r0/r1 position so that it doesn't overlap with the snp track.

<plot>

type = highlight

file = indel.txt

r0   = 0.80r

r1   = 0.80r+50p

stroke_thickness = 1

stroke_color     = black

fill_color       = black

</plot>

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[ajay kumar]

Dear Sir,

Thank you very much for your prompt suggestion, now i can able to make the desire images.

Sir i need you guidance in one more aspect sir i want to show some snp postion in different color on the same chromosome i.e. on chromosome 1 few snp in green color and rest of the snp in the blue color. is it possible if yes how i can do that

waiting for your valuable suggestion.

Thanks once again

Ajay

On Sunday, March 17, 2013 2:26:20 AM UTC+5:30, Martin wrote:

You're almost there. Just add another <plot> block, associate it with the indel.txt file and change the r0/r1 position so that it doesn't overlap with the snp track.

<plot>

type = highlight

file = indel.txt

r0   = 0.80r

r1   = 0.80r+50p

stroke_thickness = 1

stroke_color     = black

fill_color       = black

</plot>

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Sat, Mar 16, 2013 at 7:48 AM, ajay kumar <ajayb...@gmail.com> wrote:

Dear All,

i am newbie and try to generate circos image of snp and indels across 12 chromosomes i have successfully generated the image which shows the distribution of snp across 12 chromosome in one ring which colored blue, now i want to show the indel (indel.txt -included in zip file) which belongs to the same organism in same circle but in the different ring with different color but could not able to generate that image i am stuck at this point from past one week. for your reference please see the attached generated image and also my complete circos folder.



your kind help is highly appreciated


Thanks

Ajay K Mahato

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[Martin Krzywinski]

Add 

fill_color=green

to the data lines for which you want the snps to be a different color.

See the tutorial on input data files in the configuration section.

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[ajay kumar]

Dear Sir,

Thankyou very much for your suggestions but this time it doesn't works for me but i have learned a lot from your prescribed section of circos tutorial. 

sir i am still stuck at this point where i can't able to show the snp in different colors at different position, for your kind perusal i am attaching the working folder in zip format.

kindly have a look at it  and if possible please do the necessary changes which will solve my problem, your help will be highly appreciated.

Thanks and Regards

Ajay K Mahato 

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[Nithu]

Hi Ajay
Even I am working on a similar issue and can you plz help me out as how did you specify your path to run the conf files .And as shown in your attached file did you put them all in the single folder and then ran the conf files.Because I am not able to generate the output and I get the error as " Error parsing the conf flles............"

Thanks

[ajay kumar]

Hi Nithu,

you do one thing like the file i have uploaded in which i kept all the files in one folder along with .conf file prepare similar folder for your circos image in the same way

now go to that prepared folder  and from there run the following command 

$perl ~/Circos/bin/circos -conf

(run this command from the folder which you have prepared and  contains all the conf files and related files)

do not give the file name or location of the conf file as you are running this command from inside the folder which contains the .conf file)

i think this will solve your problem, if not feel free to ask


Thanks

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--

Ajay Kumar Mahato
(Research Associate)

International Wheat Genome Sequencing Project
National Research Centre on Plant Biotechnology
(www.nrcpb.org)
Indian Agricultural Research Institute, Pusa Campus
New- Delhi -110012

Contact No. +91- 9868303571

[Sandip Kale]

Hello Ajay,

I would also like to do same analysis. However, somehow, I didn't get the expected output. I am sending you the input files and output I received. I request you to please go through it and suggest corrections

Thank you in advance

With best 

Sandip

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[Martin Krzywinski]

You need to include the karyotype file for the pigeon pea for us to be able to reproduce this example.

When you say you didn't get the expected output -- what did you see and how was it different from what you expected?

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Sandip Kale]

Hello Dr. Martin,

Thank you very much for reply. 

Let me first explain the project in brief. We have identified SNPs from 8 varieties and would like to show their distribution using Circos and also show common SNPs from all 8 varieties. Initially, I tried with two variety SNP data, however, I only got ticks for chromosome 10 and 11. I am sending the karyotype file and the image I got. I request you to kindly go through it and please let me know your suggestions

With best

Sandip

Sandip

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[Duleep Samuel]

Dear Martin, a humble request,So many tips you have kindly given in these emails, thanks, will you please consider making available some 100 conf files with associated karyoptype data (from simple to complex graphs) so that I can download run the code and learn  better(apart from the tutorials), thanks, Samuel, Bangalore, India

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[Martin Krzywinski]

I didn't seen an image included in your message.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Sandip Kale]

Hello Dr. Martin,

I am sorry for that, Image is attached here. Kindly go through it and please suggest the corrections

With best

Sandip

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[Martin Krzywinski]

Your data files use a padded chromosome number

hs01 8186 8186

hs01 8380 8380

hs01 24025 24025

...

but looking at the image I suspect your karyotype.pigeonpea.txt does not (you didn't include this file). Thus, your data is referring to chromosome names that aren't actually defined.

The "hs" prefix is used to mean homo sapiens, conventionally in Circos. Other species' chromosomes are prefixed with the genus/species rather than "chr". If you want to stick to this convention (you should) I recommend that you rename your chromosomes to ppN (e.g. pp1, pp2, pp3), or use the Latin name to form the prefix.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

[Martin Krzywinski]

I'm still not sure what you're trying to achieve. If you want to color the highlights selective you have two options. Either include the color in the data file

e.g.

hs12 26880232 26880232 fill=green

or write a rule in the <plot> block that will change the color based on some condition

<rules>

<rule>

condition = on(hs12)

fill = green

</rule>

</rules.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Thu, Jun 12, 2014 at 10:52 PM, Sandip Kale <vska...@gmail.com> wrote:

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[Sandip Kale]

Hello Dr. Martin,

Thank you very much for suggestions. It solved the problem.

With best

Sandip

Sandip

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[ss]

Hi Dr Martin,

I have similar issue as per subject. I would like to see different SNP with different colors. I have added the fill_color column to my input data. However, it does not showed the color as stated in my data input.

Kindly advise what could be the issue? Hereby, I attached the required file for troubleshooting.

Many thanks
SS

[Martin Krzywinski]

You are showing the entire genome and attempting to draw a highlight of 1 bp in size. This is going to be much *much* smaller than a pixel. 

The red you're seeing is not the fill (because the element is essentially zero width), it's the outline stroke, since the thickness of this characteristic is defined by pixels.

If you want to keep the SNP elements 1 bp in size, you want to change the stroke_color to change their color.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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