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Old 07-04-2017, 07:25 AM   #1
meriem
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Default circos karyotype file

hello, I'm trying to run Circos for genome comparaison of my bacterial genomes, but i can't understand how does is work, how can I make the karyotype file from my fasta and GBK files? can anyone help me

thanks
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Old 07-04-2017, 03:56 PM   #2
neavemj
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The karyotype file lays out the 'backbone' co-ordinates for your plot. For example, if your bacterial genome has been assembled into a single 3000000 bp contig, the karyotype file could just contain a single line:

chr - chr1 1 0 3000000 black

If your assembly contains multiple contigs, then you add another line for each contig and give its size. Then the other plotting options (coverage, etc.) are aligned to these karyotype backbones. For example, to add gene regions to the plot, you would have another file with those particular co-ordinates:

chr1 1573 3503
chr1 11322 13754
chr1 14687 18718
etc.

Note that this format is pretty similar to a 'gtf' file. If one of those is available for your genome, you could just cut out the columns that give the contig name, and start and end positions of the gene.

Also check out the circos tutorials (http://www.circos.ca/documentation/tutorials/) which are very useful.

Good luck!

Matt.
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Old 07-05-2017, 03:36 AM   #3
meriem
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thank you very much for your reply, but how can i creat a GTF file from fasta or GBK files .. i don't know the start or the end of my contigs ?
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Old 07-05-2017, 02:50 PM   #4
neavemj
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The start of your contigs will be "0", and the end will be the length of the contig. For example, the karyotype file should look like:

chr - chr1 1 0 3000000 black
chr - chr2 2 0 256120 black
chr - chr3 3 0 230776 black

Do you know the length of your contigs? This should be available on NCBI or a little python script should do the job.

If you want to indicate genes in your plot, then the GBK file should have this information. Again I would use python, and in particular biopython (biopython.org), because they have functions to read GBK files and output gene co-ordinates, etc.

I think to use Circos effectively, knowledge of a scripting language is really useful to get the data into the right format..

Best,

Matt.
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Old 07-30-2017, 05:18 AM   #5
meriem
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hello Matt,
thank you for taking time to reply,
I'm still a bit confuse about circos, i coudn't find anywhere how to insert my sequences file.
does it use only the karyotype file without any other information about the sequences, if yes how does it built the mapping circuls?

thanks again
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Old 07-31-2017, 08:13 PM   #6
neavemj
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Hi Meriem,

Yes, the backbone of the plot is created using only the karyotype file. Other information, such as gene location, etc., are added using different files. You need a 'config' file, which specifies the location of the karyotype file and other information that you want to include.

I would highly recommend going to the circos tutorials as provided in the link above, and working through the examples.

Best,

Matt.
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