FPBcirc vs FPBlinear comparison from different sequencing data

[bounlu]

Hi,

I have two sets of sequencing data for the same cell lines:

1. Total RNA-Seq (ribo-)
2. circRNA-Seq (ribo- and RNaseR+)

Referring to the CLEAR article, it says:

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:

1. FPBlinear score from RNA-Seq
2. 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?

Thanks a lot.
@xingma

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Have you tried CSI NGS Portal yet?