You'll have to create a custom circos plot background (in my example GRCm38.cyto) using the length of the miRNAs and predictive genes. Then create a matrix with name_miRNA/start_miRNA/end_miRNA/name_gene/start_gene/end_gene (in my example my_data).
You can use expectation value <=3 to obtain significant miRNA/target pair from psRNAtarget result.
Here, Maximum expectation as explained in psRNAtarget help is as follows:
Expectation value is the penalty for the mismatches between mature small RNA and the target sequence. A higher value indicates less similarity (and possibility) between small RNA and the target candidate. The default penalty rule is set up by the scoring schema. Maximum expectation is the cutoff; any small RNA-target pair with an expectation less than the cutoff will be discarded in the final result. The recommended values are 3.0-5.0 depending on the scoring schema.
And why you are not using Circos tool for representing miRNA and its target?
The publication which you have referred, there also they have used circos tool for its representation.
Circlize would be suitable for this, extensive documentation available on https://jokergoo.github.io/circlize_book/book/introduction.html#principle-of-design
Hi Sej, Thanks for your comment. Can you suggest me the input data to create such plots Thanks in advance
I think you should try to recreate the figure 2 using Circlize package. It is often the best way to get started and familiarise yourself with a new package.
I know RCircos package, which works pretty well. I use it to display double stranded breaks events. Could you develop what you want to achieve and what are your data please ?
I would like to prepare a plot similar to Figure 2-Circos plot between the three predicted miRNAs and their targets. of this paper doi: 10.1016/j.gdata.2015.09.005 paper I have 10 miRNAs and respective predictive genes from TargetScan. What are the input data to create circos plots. e.g. hsa-miR-27b-5p, and hsa-let-7f-5p Thanks