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Protocol publication

[…] sis of circRNA determine their temporal-spatial specific accumulation, and contribute to their biological function in certain circumstances. However, it is almost totally unknown in this important aspect for circRNAs, though a conformed evidence has shown that a circRNA, CDR1as, can be negatively regulated by miR-671 through Ago2-mediated endocleavage pathway (Hansen et al., ). Identification of factors such as ribonucleases responsible for the degradation of circular RNAs in the cell may be a key and fundamental question., With the continuous decrease of sequencing cost, RNA-seq become the most prevalent method for identification of circRNAs. Although a few bioinformatic algorithms such as MapSplice (Wang et al., ), TopHat-Fusion (Kim and Salzberg, ), and CIRI (Gao et al., ) were developed for global discovery of circular RNAs, the consistency of these computational tools remains relatively low. RNase R treatment largely removes the false positive results, however, this strategy also impairs the quantitative feature of the circRNAs, especially the co-expression correlation between circRNAs and their parent genes. Furthermore, how to accurately quantify the expression of circRNAs is still a challenge since existing methods only count the junction reads, which are easily affected by multiple factors such as sequencing depth, read length, and fragmentation condition during RNA-seq library construction. A comprehensive comparison of existing comp […]

Pipeline specifications

Software tools MapSplice, TopHat-Fusion, CIRI