I'm working on comparing circRNAs obtained via microarray analysis and RNA-Seq for a given group of multiple sclerosis human samples.
Microarray analysis categorize the different circRNAs as exonic, intronic or sense overlapping (if the circRNA transcribed from the same gene locus).
For RNA-Seq analysis I align the reads with STAR and annotate the circRNAs with CIRCexplorer2 (just how it is described in the CIRCexplorer2 home page: https://circexplorer2.readthedocs.io/en/latest/ . I downloaded the hg19 reference and annotation files from USCS (fasta, gtf and genePred).
When I compared both results, I found out that no circRNA categorized as intronic or sense overlapping was detected by CIRCexplorer2 algorithm.
Does anyone have ever a problem like this? If yes, does anyone know if it is because of CIRCexplorer2 itself or maybe different annotation files are needed? Also, if somebody knows about other circrna prediction tools that avoid this problem could help me.