Tool: CircTools: Softwares for Discovering circRNA-microRNA Interactions from CLIP-Seq Datasets
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2.4 years ago by
lsp03yjh800 wrote:

Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechanisms and functions of most of circRNAs remain largely unknown.

We developed three stand-alone computational softwares, including circSeeker, circAnno and clipSearch, to identify and annotate circRNAs and their interactions with microRNAs (miRNAs) from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, eCLIP, irCLIP, CLASH) and RNA-seq data.

In addition, we developed interactive Web applications to evaluate circRNA-miRNA interactions identified from CLIP-Seq data and discover the miRNA-sponge circRNAs.

The software (Source Codes) and platform are available at

The paper and the protocol described these software has been published in Methods Mol Biol.

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ADD COMMENTlink modified 2.3 years ago • written 2.4 years ago by lsp03yjh800

Looks interesting - thanks

ADD REPLYlink written 2.4 years ago by Kevin Blighe65k


Thanks for your nice contribution.I have a question that I think you can help me. my question is how can I find expression level of Circular RNA via RNA-seq Data? In the other word, is it possible to find expression level of Circular RNA from RNA-seq or not? if possible,so how and by which method?

I appreciate if you share your comment with me.

Best wishes,


ADD REPLYlink written 2.3 years ago by modarzi120

Your question has been answered here: A: how to calculate or extract Circular RNA expression via RNA-seq data

You can also try the above program, which also identifies circRNAs and quantifies their expression, although that is not the main focus of the program.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Kevin Blighe65k

If any of these do not quantify gene expression for you, then you can just obtain the circRNAs co-ordinates as GTF or GFF format, and then quantify expression over these with HTseq, Kallisto, featureCounts, or Salmon

ADD REPLYlink written 2.3 years ago by Kevin Blighe65k
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