plot a diagram or graphic representation of the sequence

Question

[kapil.joshi036]

Hi all, I am working on the diseases related to mitochondrial mutation where data is generated from the CAPILLARY Sequencer. When i map the ab1 file with the mitochondrial genome i get the bam file by which i can get to know the co-ordinates of it with the help of bamTOBed . Is it possible to show where the query sequence lies into a whole genome like circos plot .

P.S I have fasta and bed file of the sequence and query

Answer 1

[Ibrahim Tanyalcin]

Dear,

You can try circos to plot the mutation as a text track. If the position is the only thing you are concerned and just want to show that you can just configure your plots file with and use vanilla circos. If you want to show other mutations with respect to conservation, amino acids etc than you will need to do bit of scripting.

I tried to address a similar problem concerning mutations in protein coding regions. Here is an example from JAK2 gene:

http://i-pv.org/JAK2.html

Is it similar to what you have in your mind?

[kapil.joshi036]

yes sir kind of that but can u elaborate circos plot n how to do it

[Ibrahim Tanyalcin]

Dear,

Im sorry for the late reply. For circos just head on to http://circos.ca/ for how to use it. However if you want to programmatically generate figures you will need to use a scripting language in conjunction.