BLAST results as an input for circos

[aman jain]

Respected sir I am new to circos and have not been able to figure out how to create an input file. Can BLAST results be used instead of BLAT

[Martin Krzywinski]

The link data format is described here

http://circos.ca/documentation/tutorials/configuration/data_files/

You will need to extract the chromosome and start/end positions for the start and end of each alignment. 

If your alignment is gapped, you need to decide whether to keep the gaps (essentially turning a gapped alignment into multiple ungapped alignments), or not.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Fri, Nov 28, 2014 at 6:21 AM, aman jain <amanjain...@gmail.com> wrote:

Respected sir I am new to circos and have not been able to figure out how to create an input file. Can BLAST results be used instead of BLAT

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[aman jain]

First of all thank you very much for the reply. In my case I have 40 ungapped bacterial chromosomes with  an average size of 5Mb. My purpose is to show orthology for a gene cluster having 21 genes. The genomes have been obtained from NCBI. I have used OrthoMCL to find orthologous clusters for the whole genomes but need to represent some of the clusters diagrammatically. Firstly is circos the right tool to do it and if yes then how to extract  start/end positions. I have already done all-vs-all Blast for the 40 genomes but the output format does match the input format for circos. You have mentioned in one of your posts that BLAT should be used, but then is this the only way. I found a  perl script with the name 'onecurcos' that performs a  BLAST and the the result is shown using circos (file attached), although incomplete but may work after some corrections. Do you think this script has some logic.

Regards

Aman Jain