How to depict Circos plot for miRNA and their targets?

Question

[itsanju87]

Can anyone suggest how can we plot miRNA and its targets using "circos plot"

Reference "An approach to identify the novel miRNA encoded from H. Annuus EST sequences", in this article the above said circos plot is done.

[Sej Modha]

Here is a really good Circos tutorial that should help you to recreate the Circos plot.

[mks002]

For the miRNA sequences first u do target prediction (miranda tool). U will get location where you miRNA are falling on your target. Then u can take these inputs in particular particular format. For each kind data input type is there. The tutorials, data and input files you can see at the link Circos Tutorial

[itsanju87]

I have predicted the targets. I don't find a template or format for this kind in the tutorial . If you can suggest, it will be very useful.

[cschu181]

You need to use links.

A link file is formatted like this: first chromosome/contig/scaffold/mirna precursor, start on first chromosome/.., end on first chromosome, second chromosome/.., start on second chromosome, end on second chromosome (s. below)

chr4A   1349160 1352160 chr2B   668145  671145
chr4A   1349160 1352160 chr2D   725761  728761 
chr2B   668145  671145  chr2D   725761  728761

start can be equal to end, so you could just use the start position of the predicted target chr start start, or you can use start and end, w/ever. For the position on the precursor, you could use the actual position of miRNA/miRNA* or you could use the middle of the sequence, check whatever looks better.

You then need to import this in your circos config file with:

<links>

    <link>
    show = yes
    file = links.txt
    radius        = 0.99r
    bezier_radius = 0r
    color         = bupu-9-seq-1
    thickness     = 17
    flat = yes
    crest = 1
    </link>
</links>

links.txt should be the path to your links file, color can take any colourmap, if you omit that parameter, then the links will be black.