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should each RNA-seq has Circular RNA?

Hi, I used CIRI2 for detecting Circular RNA from Paired-end RNA sequencing. I have 114 samples. Up to now, I run CIRI2.pl for 3 SAM file which they are the output of Burrows-Wheeler Aligner (BWA). the output of that 3 RNA-seq has no any Circular RNA.

based on the computational and also biological approaches, is it possible that RNA-seq has no Circular RNA? If no, how should I do for solving this problem?

I appreciate it if anybody shares his/her comment with me.

Best Regards,

alignment rna-seq circular rna ciri2
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updated by medstarrehabilitation • medstarrehabilitation • written by modarzi modarzi

Not an expert in this at all, but according to Wikipedia circs are not polyadenylated, so if this is standard polyA-selected RNA-seq it is expected not to see any. I suggest you read papers who described these types of RNAs and see which types of libraries they used and which tools. I doubt bwa is a good tool (non splice-aware).

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written by ATpoint ATpoint

Thank you @ATpoint. For bwa I agree with you but it is CIRI2 protocol. Individually, HISAT2 is the best choice for RNA-seq alignment but CIRI2 doesn't accept SAM file generated from HISAT2. it works just by SAM file which produces with bwa. I have no doubt about the CIRI2 pipeline. I want to know, biologically, is it possible that RNA-seq has no Circular RNA?

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written by modarzi modarzi

I gave you a "biological" answer above.

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written by ATpoint ATpoint

You mean I have to expect that some RNA-seq has no Circular-RNA?

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written by modarzi modarzi

I guess so.

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written by ATpoint ATpoint

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