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?
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.