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DOI: 10.7717/peerj.2934/fig-7

This study presents a new tool to help further characterize circRNA candidates. Our tool, FUCHS, is able to identify alternative exon usage within the same circle boundaries, summarize the different circles emerging from the same host-gene, quantify double-breakpoint fragments as indicator for circularity and visualize a circRNA’s read coverage profile independent of any genome browser.

When over-expressing circular isoforms to gain insights into the function or biogenesis of the target circRNA it is crucial to know the exact exon structure in order to express only the desired isoform. Furthermore, integrating knowledge about the exact exon structure could lead to a more accurate differential motif enrichment and miRNA seed analysis. Information about double-breakpoint fragments and coverage profiles of a circRNA can be used to filter out likely false positives e.g., if a circRNA is supported only by single-breakpoint fragments, although the circle is shorter than the fragment length, thus if it was a true circRNA it should be supported by double-breakpoint fragments. Plotting the individual coverage profiles allows the user to quickly examine all circles to get a general idea about coverage, length and number of exons, as a first quality measure of the data.

Altogether FUCHS is a valuable tool to characterize circRNAs. FUCHS provides the user with directions for further steps to investigate the circRNA’s function and biogenesis.

The authors declare there are have no competing interests.

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performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

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performed the experiments, contributed reagents/materials/analysis tools.

Chistoph Dieterich conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

The following information was supplied regarding data availability:

GitHub: https://github.com/dieterich-lab/FUCHS/tree/master/GCB_testset .

We have made all samples available. All HEK293 RNA-seq data sets are available via SRA study SRP050149 ). All murine RNA-seq data sets are available via SRA study SRP097141 .

FM and CD acknowledge funding by the DFG Priority Program SPP1738 (DI 1501/5-1 to CD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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