Dear Arijit,

To prepare the input files for Circos, usual command-line tools like awk will help you shaping them (bed files, arcs, etc) according to what Circos need (described in the documentation / available examples / Circos courses). So you can simply use Excel, R, python... I don't think specific tools are required for printing specific columns of the usual beds, bedgraphs and so on.

Read the well-made Circos courses (http://circos.ca/tutorials/course/), check the examples of input data for what you desire (bedgraphs, beds and so on), and format the data with the tool you know the best.

If you mean, automatically preparing the conf files, Circos courses are quite useful for that and a copy pasting the examples are sufficient to start building your Circos plot.

Otherwise, if you don't want to spend some time learning the free command-line based version of Circos, more user-friendly approaches exist but you have to pay for it, like Circa: http://omgenomics.com/circa/

There's also a Galaxy Wrapper for Circos available here: https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos

You can use it on the free European Galaxy server: https://usegalaxy.eu/

I don't recommend RCircos, it is quite limited.

However, there's a much better R alternative: Circlize, which is as good as Circos. The documentation is accessible here: https://jokergoo.github.io/circlize_book/book/

As a sidenote, you can also consider pyGenomeTracks (https://github.com/deeptools/pyGenomeTracks) for plotting data along whole chromosomes really easily and in very nice ways. If need the "circular view" of Circos, then imagemagick will do that for you (http://www.imagemagick.org/Usage/distorts/#map_circlar_arc). PyGenomeTracks can also display arcs, and even Hi-C heatmaps, which Circos is not currently capable of.

Good luck,

Gautier

Hey Arijit Ghosh,

There are a few packages on R that allow you to create Circos plots, but my personal favorite is Circlize. It is more intuitive to me. I am attaching a figure I created for my recent paper: https://www.nature.com/articles/s41374-018-0104-x.

In the supplemental methods, I have also included all of the scripts used to create the Circos plots (along with other analyses). Please cite me if you decide to use it!

Below is the R script for creating this plot:

library(circlize)

library(gtools)

library(dplyr)

om = circos.par("track.margin")

oc = circos.par("cell.padding")

circos.par(track.margin = c(0, 0), cell.padding = c(0, 0, 0, 0))

circos.par(start.degree = -250)

circos.initializeWithIdeogram(track.height = 0.05)

### Labels for inversely changing DMRs with DEG

circos.genomicLabels(Gene_Labels, labels.column=4, side='outside', cex=0.38)

## Add CpG Island Lines here (blocks to tell the reader where the CpG Islands are located?)

# Methylation Density

DMR.PerChange