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Question: Is circular RNA read out as linear fragments during Rsubread-DESeq2
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gravatar for csijst
5 months ago by
csijst0
Singapore/National University of Singapore
csijst0 wrote:

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?

ADD COMMENTlink modified 5 months ago by Wei Shi2.9k • written 5 months ago by csijst0
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gravatar for Michael Love
5 months ago by
Michael Love20k
United States
Michael Love20k wrote:

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.

ADD COMMENTlink written 5 months ago by Michael Love20k

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.

ADD REPLYlink written 5 months ago by csijst0
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gravatar for Wei Shi
5 months ago by
Wei Shi2.9k
Australia
Wei Shi2.9k wrote:

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.

ADD COMMENTlink modified 5 months ago by Gordon Smyth35k • written 5 months ago by Wei Shi2.9k

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.

ADD REPLYlink written 5 months ago by csijst0
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