Demystifying Long-Read RNA-Seq Analysis with FLAIR in OmicsBox
Fabian Jetzinger, Doctoral Candidate at BioBam Bioinformatics, explains how to reconstruct, curate and quantify transcriptomes with FLAIR within OmicsBox 3.5.
Long-read sequencing technologies such as PacBio and Oxford Nanopore are reshaping transcriptomics by revealing full-length isoforms and complex splicing events. But how can researchers distinguish true transcripts from artifacts?
In this new article, Fabian walks through an integrated workflow that combines FLAIR, one of the best-performing tools in recent benchmarks such as the LRGASP challenge, with SQANTI3-based quality control. Everything is configured from the OmicsBox interface, without manual setup or coding.
What You Will Learn
What You Will Learn
- Transcriptome reconstruction with FLAIR: the four steps of the pipeline (align, correct, collapse and quantify) and the input data you need: long reads in FASTQ, a reference genome, and reference annotations and/or short-read data.
- Configuring FLAIR in OmicsBox: how to set up the wizard, when to provide pre-aligned reads, and why Stringent Mode and Check Splice Sites are recommended for well-annotated model organisms.
- Curation with SQANTI3: how to flag artifacts and keep only high-quality transcripts, using the machine-learning filter when orthogonal data are available or the rule-based filter otherwise.
- Re-quantification: how to re-run FLAIR on the curated transcriptome so the count table reflects only validated transcripts, ready for differential gene or transcript expression analysis.
Why This Matters
No single gold-standard tool has emerged for long-read transcriptome reconstruction, and the right choice depends on the dataset and the research goals. By integrating FLAIR and SQANTI3 in a single workflow, OmicsBox simplifies long-read RNA-seq analysis and enables high-confidence isoform discovery in both model and non-model organisms.
📖 Read the full post here: https://www.biobam.com/demystifying-long-read-rna-seq-analysis-with-flair/
No single gold-standard tool has emerged for long-read transcriptome reconstruction, and the right choice depends on the dataset and the research goals. By integrating FLAIR and SQANTI3 in a single workflow, OmicsBox simplifies long-read RNA-seq analysis and enables high-confidence isoform discovery in both model and non-model organisms.
📖 Read the full post here: https://www.biobam.com/demystifying-long-read-rna-seq-analysis-with-flair/
