Quantifying circular RNA expression from RNA-seq data using model-based framework

Abstract

Supplementary data are available at Bioinformatics online.

CircRNAwrap – a flexible pipeline for circRNA identification, transcript prediction, and abundance estimation

“…Most previously described circRNAs originated from the same splice sites as known exon locations but more recently discovered circRNAs occur at different splice sites from the linear isoforms. Similar to the estimation of linear RNA abundance estimation with Sailfish, Sailfish-cir predicts the abundance of cir-cRNAs and differs from previous tools, which use backsplice reads for circRNA abundance [30]. This information will enable scientists to perform miRNA motif discovery and seed analysis, allowing analysis of potential regulators for biogenesis of circRNAs.…”

“…Currently, RNA-Seq data is used to estimate cir-cRNA expression by measuring the abundance of expression profiles of circular and corresponding linear isoforms. The modified Sailfish pipeline could include both linear and circular transcripts to interpret RNA-Seq data [30].…”

“…CircRNA sequence prediction tools included CIRI-AS [26], CIRC-explorer2 [27], and RAISE [28]. To estimate the circRNA abundance with the merged circRNA tools, we used Sailfish-cir [30]. We used RAISE for circRNA inner splice analysis, which combines different tools.…”

“…Previous methods only considered the backsplice reads when calculating the circRNA abundance, which gives a biased estimate, especially for some low abundance circRNAs. In order to estimate the abundance of circRNA transcripts as linear RNAs, Sailfish-cir uses the modelbased algorithm Sailfish to quantify circular transcripts based on the pseudo-linear transcript [30,43], giving the coverage and depth across the whole transcript.…”

“…These tools, such as CIRI-AS, FUCHS, and RAISE, use the splice and paired-end mate reads information to build whole coverage of circular transcripts [26,29]. The modified Sailfish pipeline could include both linear and circular transcripts to interpret RNA-Seq data [30]. Currently, RNA-Seq data is used to estimate cir-cRNA expression by measuring the abundance of expression profiles of circular and corresponding linear isoforms.…”