Circos-How To Generate Circos Image Of Snp And Indel Across Chromosomes

Question

[ajaybioinfo]

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

[Michael]

You might want to make your files available, this sounds like a mailing list cross-posting though. Did you post this on the circos mailing list.

Answer 1

[VS]

This question has already been answered here earlier on mailing list : https://groups.google.com/forum/#!msg/circos-data-visualization/0HDZHNVCxvk/Z9wECrRZZRYJ

Answer 2

[Rahul Sharma]

Hi,

What kind of ring you want to add? there are lot many options to present your data: Scatter plots, histograms, lines, heatmaps or tiles? You will have to generate a new text file, having the following format:

Format: chr start end value [options] ... Chr3 196000000 197999999 71.0000

Chr3 198000000 199999999 57.0000

Chr4 0 1999999 28.0000

Chr4 2000000 3999999 40.0000

Chr4 4000000 5999999 59.0000 ...

Chromosome names should be same both of the files. You can also visit this link: http://circos.ca/documentation/tutorials/2d_tracks/tiles/configuration

Hope this will be helpful.

Wishes, Rahul