Is circular RNA read out as linear fragments during Rsubread-DESeq2
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csijst • 0
@csijst-15102
Last seen 2.6 years ago
Singapore/National University of Singap…

May I clarify a part of the DESeq2 package? Is it true that DESeq2 counts for linear (only) transcripts and excludes any possibility in circular RNA (circRNA)? In which, an increase/decrease in circRNA has no effect on the number of counts produced in the results/output? Or does DESeq2 not able to distinguish the two, will assume circRNA as linear fragments, and include it into the counts?

deseq2 circrna rsubread • 548 views
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@mikelove
Last seen 48 minutes ago
United States

DESeq2 has not concept of linear vs circular transcripts. You provide the software with a matrix of counts and it compares across samples, adjusting for e.g. library size.

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That I can understand. I believe the Rsubread is the one featuring the reads. But wanted to clarify at least before I lay the information on my colleagues.

Thanks by the way.

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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 14 hours ago
Australia/Melbourne/Olivia Newton-John …

If you used Rsubread featureCounts to generate counts, the mapped reads are just assigned to overlapping genes. It doesn't matter whether the genes are located on a linear sequence or on a circular sequence.

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This is good information. So what you mean is that Rsubread will use the annotations (from the gtf file) to gather information of a location, and count the number of reads that cover that area yes? In which, the reads could encompass either linear or circular RNA? Am I right to say that if the DESeq2 shows like an increased log2foldchange in a treated condition (as compared to a control), it could mean either the linear RNA is increasing, or both linear & circRNA? I know this might sound silly but don't mind me asking - Will there be any hypothetical idea that the log2foldchange would stay consistent (linear RNA does not change through qRT-PCR) but circRNA is actually increasing (let's consider the scenario that the circRNA has a robust expression)?

Thank you.

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