Different from poly(A)+ RNA-seq datasets that are used to detect polyadenylated cognate linear RNAs, all three types of non-polyadenylated RNA-seq can be used to determine circRNA expression by FPB. However, only ribo− RNA-seq datasets that profile both polyadenylated linear and non-polyadenylated circular RNAs in parallel are suitable for direct circular and linear RNA expression comparison by CIRCscore. In contrast, in poly(A)−/ribo−, and RNase R-treated RNA-seq datasets, polyadenylated linear RNAs are largely depleted, which is unsuitable for accurate linear RNA quantification and subsequent CIRCscore evaluation.
It means I cannot compare circRNA expression to linearRNA expression directly in either of these datasets by utilizing CIRCscore. Rather, I would like to compare them by calculating:
FPBlinear score from RNA-Seq
FPBcirc score from circRNA-Seq
Does this make sense? Are they comparable since they are derived from the same cell lines although they come from different sequencing data? Do I need additional normalization step?
Hi,
I have two sets of sequencing data for the same cell lines:
Referring to the CLEAR article, it says:
It means I cannot compare circRNA expression to linearRNA expression directly in either of these datasets by utilizing CIRCscore. Rather, I would like to compare them by calculating:
Does this make sense? Are they comparable since they are derived from the same cell lines although they come from different sequencing data? Do I need additional normalization step?
Thanks a lot. @xingma
Have you tried CSI NGS Portal yet?