circos input data

[bsp017]

Hi all,

I want to display my assembled and annotated bacterial genomes in circos. I have the program set up on my system and practiced several of the online tutorials. However do I have to write my own custom scripts to get my data (i.e. FASTA, GFF, etc files) into the native circos format?

Is there an easier way to produce a simple circos plot i.e. GC content, genome, aligned genes? There are some scripts available on the circos website but these are quite specific.

Thanks,

James

[Cytosine]

Parsing your data into a proper format should be pretty straightforward and you can help yourself with sample files from the website.

If you want an easier way, then you should use an alternative program.

[ECO]

Parsing your data into a proper format should be pretty straightforward and you can help yourself with sample files from the website.

If you want an easier way, then you should use an alternative program.

Help him, or don't post. The above post is not productive. I have found Circos to be frustratingly poorly documented in the past as well...so he's not alone in needing help.

[Cytosine]

Help him, or don't post. The above post is not productive. I have found Circos to be frustratingly poorly documented in the past as well...so he's not alone in needing help.

I tried to help by telling him to use sample files as a guideline... as that is exactly what I have done myself when I started with Circos and I still do every time when I make a new visualization.
There is nothing that would be unconstructive in this sentence, as it is a genuine tip I give to everyone else that asks me about Circos.

Circos may be a badly documented piece of software that is hard to get up and running, but don't take it out on me, because of that.

And btw., I am not familiar with scripts on the circos website, so I cannot comment on that one.

[blakeoft]

bsp017,

Have you looked into RCircos? I too have struggled with Circos in the past (so much so that I never managed to do anything meaningful), but I think RCircos might be a little easier to use. I can't guarantee that it does what you want it to, but it might be worth a try if you've never looked at it.

http://cran.r-project.org/web/packages/RCircos/vignettes/Using_RCircos.pdf

[bsp017]

blakeoft,

I had a look at Rcircos but it has built in ideograms for human, rat and mouse chromosomes. So I didn't think it was suitable for my bacterial data. It would have been ideal as it parses data and returns it in the circos interval format. This is my difficulty with circos as I don't know how to write code.

Just to clarify my original post; if I wanted to use circos I would have to learn a language such as perl or awk to parse my data into circos format or are there other tools available.

Thanks