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Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have heard about circRNA finder, find circ, CIRCexplorer, CIRI, and MapSplice which all are different programs to find circRNA, but I really don't know which one is the most used and easy to use, and which one is most accurate for finding circRNA.

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    $\begingroup$ Welcome to SE Biology. Just to let you know why I changed "algorithm" to "program". An algorithm is the strategy by which a problem can be solved computationally, a program is its implementation in code. You would ask about the best algorithm if you wanted to write your own implementation or you knew which algorithms the different programs you mention used and wished to choose from those using the best algorithm. I assume that in fact you just want recommendations from the programs named. $\endgroup$ – David Apr 15 '17 at 8:46
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According to the most recent paper (https://doi.org/10.1093/bib/bbx014), CIRI2 shows a balanced performance on sensitivity and FDR.

"Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage."

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