# Protocol for accurately annotating circular RNA and microRNA in giant vertebrate genomes

## TL;DR

This paper introduces a protocol for accurately identifying circular RNA and microRNA in large vertebrate genomes using genomic and transcriptomic data.

## Contribution

A stepwise framework for adapting tools and minimizing false positives in repeat-rich giant genomes.

## Key findings

- The protocol includes quality checks to reduce false-positive predictions in repeat element-rich genomes.
- It provides procedures for adapting existing tools to work with giant vertebrate genomes.
- The method is applicable to the annotation of non-coding RNAs in large genomes like those of salamanders and lungfish.

## Abstract

With the advent of long-read sequencing techniques, there has been an increase in the sequencing and assembly of giant genomes such as salamanders and lungfish. Here, I present a protocol for accurately annotating non-coding RNAs, specifically circular RNAs and microRNAs, using genomic and transcriptomic data. I describe quality checks and post hoc steps to minimize false-positive predictions in repeat element-rich genomes. This protocol has potential application for annotating non-coding RNAs in other giant vertebrate genomes.

For complete details on the use and execution of this protocol, please refer to Brown et al.1

•Stepwise framework for annotating circular RNA and microRNA•Procedures for adapting existing tools for giant vertebrate genomes•Detailed quality checks for limiting false-positive predictions

Stepwise framework for annotating circular RNA and microRNA

Procedures for adapting existing tools for giant vertebrate genomes

Detailed quality checks for limiting false-positive predictions

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

With the advent of long-read sequencing techniques, there has been an increase in the sequencing and assembly of giant genomes such as salamanders and lungfish. Here, I present a protocol for accurately annotating non-coding RNAs, specifically circular RNAs and microRNAs, using genomic and transcriptomic data. I describe quality checks and post hoc steps to minimize false-positive predictions in repeat element-rich genomes. This protocol has potential application for annotating non-coding RNAs in other giant vertebrate genomes.