Sailfish-cir

Sailfish-cir quantifies circular RNA (circRNA) expression from RNA sequencing (RNA-seq) data to enable accurate estimation of both circular and linear transcript abundances.

Key Features:

• Transformation Strategy: Converts circular transcripts into pseudo-linear counterparts to enable model-based quantification using algorithms such as Sailfish.
• Dual Quantification: Simultaneously estimates expression levels of both linear and circular transcripts from RNA-seq data.
• Performance Factors: Quantification accuracy is influenced by gene length, expression amount, and the ratio of circular to linear transcripts.
• Superior Performance: Demonstrates improved estimation of circRNA expression compared with count-based tools on simulated and rRNA-depleted RNA-seq datasets.
• Improved Linear Transcript Accuracy: Accounting for circular transcripts increases the accuracy of linear transcript expression measurements.

Scientific Applications:

• CircRNA expression profiling: Enables quantitative profiling of circRNAs across samples to study their abundance and distribution.
• Comparative analyses: Supports comparisons between circular and linear transcript expression to assess their relative contributions.
• Functional inference: Facilitates investigation of circRNA roles in biological processes and diseases by providing reliable expression estimates.
• Tissue- and cell type-specific studies: Allows exploration of tissue- and cell type-specific circRNA expression patterns to identify potential regulatory mechanisms.

Methodology:

Transforms circular transcripts into pseudo-linear forms and applies model-based quantification (e.g., Sailfish) to simultaneously estimate circular and linear transcript expression from RNA-seq data.