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What is the best tools for circRNA analysis (extraction and quantification) ?

Good day everyone!

I am a Bioinformatician and am working on circRNAs at my job.

Since circRNAs are a hot topic right now, I thought I could ask Biostars forum how people are working on them.
(I have asked on r/bioinformatics a couple of days ago, but despite some upvotes, I got no answer)

Currently, I have been using CIRIquant for the extraction of BSJ from RNA-seq data and subsequently I do a DE analysis to extract DE circRNAs.

I would like to ask you if CIRIquant is the most reliable tool for this task or there are better tools.

Also, since CIRIquant extract only BSJ, what about the reconstruction of circRNA ?
I have used the R package circRNAprofiler, but looking at the code it seems it is just concatenating internal exons defined by the BSJ: (e.g. chr9:3390000-3390000, all the exons between 3390000 and 3391000 in chromosome 9).

Also, in circRNAprofiler, all the annotated BSJ that end up containing more than one gene are not reconstructed. Is this because they are all considered as false positive ?

programming rna workflow
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written by chloelaloe • chloelaloe

1 answer

https://www.biostars.org/p/333090/ and a paper included there.

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written by GenoMax GenoMax

Thank you for the paper.
I skimmed it but it is from 2017. Among the softwares they compare there is CIRI and CircExplorer, both of which we now have version 2 (CIRI2, and CircExplorer2).
I am saying this because CIRIquant is from the same authors of CIRI1/2 and it is based on CIRI2 for the extraction of the BSJ.
They have reduced the number of false positive with respect to using only CIRI2.
I wanted to know if someone else was using it, or using something else. If there is some best pratice (like some filtering after the extraction, e.g. filter all BSJ not present in at least 2 sample, or with occurences lower than 2)

And also how they are dealing with the reconstruction of the circRNA.

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written by chloelaloe • chloelaloe

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