NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs)...

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Non-co-linear (NCL) transcripts, including circular RNAs and fusion RNAs, exhibit topological inconsistencies with the reference genome.
• Existing RNA-sequencing (RNA-seq) based detectors identify numerous NCL events, but discrepancies among tools suggest a high rate of false positives.
• A systematic method for evaluating the reliability of detected NCL events is lacking.

Purpose of the Study:

• To develop a computational tool, NCLcomparator, for the systematic post-screening of NCL events.
• To provide a reliable metric, the NCL score (NCL _score), to assess the confidence of identified NCL events.
• To assist researchers in selecting high-confidence NCL events for functional investigation.

Main Methods:

• NCLcomparator analyzes NCL events identified by various detectors using paired-end RNA-seq data.
• It assesses potential false positives arising from ambiguous alignments, such as alternative co-linear explanations or multiple genomic matches.
• The NCL score is defined based on the variation in supporting NCL junction reads, with higher scores indicating greater reliability.

Main Results:

• NCLcomparator effectively distinguishes between genuine NCL events and those likely resulting from alignment artifacts.
• Events derived from ambiguous alignments typically exhibit lower NCL scores compared to other NCL events.
• The software provides supplementary metrics including expression levels and junction usage to aid in selecting highly confident NCL events.

Conclusions:

• NCLcomparator offers a systematic approach to filter and prioritize NCL events identified by different tools.
• The tool facilitates the selection of high-confidence NCL events for downstream functional studies, advancing research in this understudied transcript class.
• NCLcomparator is freely available at https://github.com/TreesLab/NCLcomparator .